Use topological sort during ProcessBundle in Java SDKHarness

In reference to comment https://github.com/apache/beam/pull/6093#issuecomment-410831830

• Use QueryablePipeline#getTopologicallyOrderedTransforms and execute processBundle requests.
• Explore: is it worth caching the sorted structure when registerRequest is received.
• Also, explore how we can handle cycles in the execution stage in process bundle request if any.