filesToStage should allow for common ways in which people package their resources

[damccorm]

Different application environments launch and maintain their classpath resources in various ways. See these SO questions for examples of how people launch their pipelines that currently are unsupported:
http://stackoverflow.com/questions/31978566/detectclasspathresourcestostage-unable-to-convert-url
http://stackoverflow.com/questions/40099952/launching-dataflow-jobs-from-a-java-application

Add support for classpaths which:

• use URLs that are embedded within other jars
• allow for manifest files that specify their classpaths
• add support for rsrc:// URIs to support Eclipse jar packaging

Imported from Jira BEAM-779. Original Jira may contain additional context.
Reported by: lcwik.