For the planner to have a notion of staging site, following needs to be done

• The compute jobs should be associated with a staging site in addition to an execution site.
• The create dir and cleanup jobs that are created need to refer to the staging site
• create dir and cleanup strategies in Pegasus need to refer to staging site.
• The transfer refiners need to use staging site associated with the compute jobs for their logic
• The SLS interfaces need to refer to staging site instead of compute sites.
• The planner needs to have a command line options to specify a staging site.
• Executables need to be staged to the staging site.
• The cleanup worklfow needs to refer to the staging site!

For 3.2 first level staging cannot be bypassed. Bypassing staging creates problems with in place cleanup and condor io file transfers.