error:Unable to install breakpoint in due to missing line number
Make sure you are setting debug=true in your compilation task, otherwise you won't be able to debug.
The solution given above involving moving your eclipse workspace to be in the app-server's directory is not a very good idea.
The issue, most likely, is that there are two compiles happening -- eclipse's and ant's. The settings for the eclipse compiler don't affect the ant build even if you launch the ant build from within eclipse. Ant controls it's own compiler settings. You can tell ant to generate debugging info like this:
Code:
<javac ... debug="true" .../>