Even if you do not want to use Maven (and I don't advocate for it), it would help to have a more common project structure:
src/main/webapp (everything that gets installed to the root of the web app)
And it helps, if the dependencies would be managed, e.g. by Ivy so that one can get a quick overview of your direct dependencies and their versions.
If you'd use Git, I could easily prepare patches to transform your project structure and build.xml to these conventions.
Regards, Thomas Koch