I have finally figured it out, the problem was with the fileset dir field. I initially had it as the project root, when I changed it to the src root it all works just fine!
A snippet of the build file that does the job follows :
<?xml version ="1.0" encoding = "UTF-8" ?>
<!DOCTYPE doc_build>
<project name="documentation" default="doc" basedir=".">
<description>
co2
doc build file
</description>
<!-- set global properties for this build -->
<property environment="env" />
<property name="srcdir" value="${env.CO2ROOT}/com/abc/co2" />
<target name="doc"
description="generate documentation from the sources " >
<javadoc
destdir="dummy"
author="true"
version="true"
use="false"
windowtitle="CO2 API" >
<fileset dir="${srcdir}" defaultexcludes="yes">
<include name="common/appmgr/*.java" />
<exclude name="common/appmgr/Security.java" />
</fileset>
<doctitle><![CDATA[<h1>Content Over Optics Documentation</h1>]]></doctitle>
<bottom><![CDATA[<i>Copyright © 2004 ABC Inc. All Rights Reserved.</i>]]></bottom>
</javadoc>
</target>
</project>