Since you are referring to a build.xml file, I'll assume you are using Ant (or Eclipse is using it for you.) If that is the case, you want to use the war Ant task and its includes attribute (or fileset nested task) to list your web directory for inclusion in the resulting war.
http://ant.apache.org/manual/CoreTasks/war.html
Assuming you are using an older Ant distribution that lacks the war task, use the jar task, which war inherits from.
I don't know what your build.xml looks like, but I would venture to guess it has a war or jar task. Using its includes attribute, it should look something like this (this is from the top of my head, you might need to tweak it to compile for your specific situation):
<war destfile="your.war" webxml="src/metadata/your.xml">
<fileset dir="src"/>
<fileset dir="web"/>
<classes dir="build/classes"/>
</war>
Without seeing your build.xml, it is impossible to tell if this suggestion is applicable or not, though.