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

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](https://issues.apache.org/jira/browse/BEAM-779). Original Jira may contain additional context.
Reported by: lcwik.

Start by locating the filesToStage implementation and reviewing the linked Stack Overflow examples and BEAM-779 context. Done means classpaths using URLs embedded in other jars, manifest-specified classpaths, and rsrc:// URIs are supported so their resources can be staged.

Written by the indexing model from the issue text.