I had the same error message in Eclipse 3.4.1, SUN JVM1.6.0_07 connected to Tomcat 6.0 (running in debug-mode on a different machine, Sun JVM1.6.0_16, the debug connection did work correctly).
Window --> Preferences --> Java --> Compiler --> Classfile Generation: "add line number attributes to generated class file" was checked. I did a clean, recompile. I did uncheck it, recompile, check it, recompile. I made sure the project did use the global settings. Still the same message.
I switched to ant build, using
Still, same message.
I didn't find out what caused this message and why it wouldn't go away. Though it seemed to have something to do with the running Tomcat debug session: when disconnected, recompiling solves the issue. But on connecting the debugger to Tomcat or on setting new breakpoints during a connected debug session, it appeared again.
However, it turned out the message was wrong: I was indeed able to debug and set breakpoints, both before and during debugging (javap -l did show line numbers, too). So just ignore it :)
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