Java applications are not stored in Apache, it can be only connected to another Java webapp hosting webserver using the mod_jk connector. mod_jk is a replacement for the elderly mod_jserv. It is a completely new Tomcat-Apache plug-in that handles the communication between Tomcat and Apache. Several reasons:
mod_jserv was too complex. Because it was ported from Apache/JServ, it brought with it lots of JServ specific bits that aren't needed by Apache.
mod_jserv supported only Apache. Tomcat supports many web servers through a compatibility layer named the jk library. Supporting two different modes of work became problematic in terms of support, documentation, and bug fixes. mod_jk should fix that.
The layered approach provided by the jk library makes it easier to support both Apache1.3.x and Apache2.xx.
Better support for SSL. mod_jserv couldn't reliably identify whether a request was made via HTTP or HTTPS. mod_jk can, using the newer Ajpv13 protocol.