Don't you need an extension to do that? Meaning you'd have to be able to change source code to or at least have additional settings available to run PHP inside apache tomcat? Let me know, I'd be keen to know.MANGODIR/overrides/web/modules/mangoUI/web/
as far as I know is the web host directory so you don't lose changes with upgrades. But then again that's for just running straight .html I suppose. Not sure if that would work for you.
Other than that I guess you'd need @terrypacker to answer this one unless another Java dev is readily available...