I am using following Ant script to create a war of simple web application.
I don't know exact answer but here is my way of using Ant build.xml for webapps. Give it a try. This works inside Eclipse or run from the command line. Few key points are:
Use this common folder structure for webapp project.
/mywebapp/ant.bat
/mywebapp/build.xml
/mywebapp/classes/
/mywebapp/src/
/mywebapp/src/META-INF/MANIFEST.MF
/mywebapp/lib/
/mywebapp/web/
/mywebapp/web/WEB-INF/web.xml
/mywebapp/web/WEB-INF/lib/
/mywebapp/web/META-INF/context.xml
mywebapp/build.xml
src/META-INF/MANIFEST.MF
Implementation-Title: myappname
Implementation-Version: 1.0.0 (2010-03-01)
Implementation-Vendor: My Name Ltd.
Implementation-URL: http://www.myname.com
mywebapp/build.bat
call c:\apache-ant-1.7.0\bin\ant.bat build
pause
Build script creates war package and manifest.mf within web-inf/lib/mywebapp.jar is updated to have build number, title and version. Very handy you can use folder content as a template for new webapp projects. Just edit build.xml to have new project name.
Some compile-time dependencies point mywebapp/web-inf/lib folder. Non war-packaged libraries are put to mywebapp/lib/ folder for compile time only. I like keeping each dependency within project version control so thats a reason for this lib folder. You may use *.jar wildcard ant syntax but I explictly list each file for self documentation purpose.
Here is a bonus file to be used in Tomcat during development time. It publishes webapp on Tomcat and any changes in project folder is seen immediately, its very handy for client file changes (html,js,jsp).
tomcat/conf/Catalina/localhost/mywebapp.xml
ps: Ant build system is fine no matter what some people may say. Go with it as you please.