Enhance setup and finish message for greater Galaxy integration.

If GALAXY_HOME is set, let client know so that paths/scripts can be constructed against it. Pass list of working directory contents back to client at end of job - this is potentially useful as a step toward remote metadata setting and handling of tools with a variable number of outputs.
Have LWR client fetch implicitly required outputs over from remote working directory.

These include output files from variable tool outputs (http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files) and files related to metadata processing.