Java 1.4 or earlier, use xdoclet, although it's hard to see how you'd
generate application.xml.  It's definitely easier to generate something
that is tightly coupled with Java source files (e.g. ejb-jar.xml)

Java 5 onwards, you can use annotations and apt (annotation processing
tool)

There may well be custom Ant tasks out there to generate one for you,
although even in that case, you'd be hardcoding the contents in Ant.

I had similar requirements and stumbled across the following blog entry
from Dan Bequeaith:
http://peeps.dallas.focus-technologies.com/roller/page/dbequeaith/20041012
(See Handy application.xml generation ant task)

The XLST stylesheet he developed should give you a good headstart.

Joe