The three jars are supersets of one another. If you jarjar aspectjtools and just use that, it has everything in (including weaver/runtime). In fact the compiler classes are only in aspectjtools.
For debugging, can you just use JVM remote debugging? Set that -Xdebug etc when launching (or in JVM_OPTS if using a script) and then attach the eclipse debugger to it?
> [WARNING] You aren't using a compiler supported by lombok, so lombok will not work and has been disabled.
> Your processor is: org.aspectj.org.eclipse.jdt.internal.compiler.apt.dispatch.BatchProcessingEnvImpl
That does sound like jarjar didn't behave. Did you 'jar -tvf' your jar and check everything had been changed back to org.eclipse.jdt?
In theory it would also be possible to build an AspectJ package that included those additional bundles lombok wants from eclipse, and jarjar those too so the prefixes are all in agreement (org.aspectj.org.eclipse.jdt). Then once that package name was supported throughout lombok it ought to all work - that is probably what would need doing to get it behaving in the Eclipse IDE too. Create an extra bundle with the prefixed forms of the JDT UI packages for use just in this context.
cheers,
Andy