eclipse and large projects - Java

I've been using eclipse for some time, and I think it's a great tool.
Although the project I work on is pretty large, for the most part I've
been able to create a project for just my small section of code. The
dependencies with the rest of the system were satisfied via a jar file.
This was adequate (though not ideal).

I now have a task that requires me to work with the system in its
entirety. The trouble I've had in the past is that the build process
is complex and requires ant. Now, I know eclipse has great ant
support, but when I compile with Ant, any stack traces I get from
exceptions don't provide file or line number information. I think I've
also had trouble with the debugger when building with ant. Is there an
option I'm missing or something?

Thanks