Use topological sort during ProcessBundle in Java SDKHarness

[kennknowles]

In reference to comment #6093 (comment)

• 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.

Imported from Jira BEAM-5090. Original Jira may contain additional context.
Reported by: angoenka.

[dakshing]

.take-issue