I'm running a workflow with:

pegasus.transfer.*.remote.sites = execution

and the remote execution site has only file:// accessible URLs:

<directory type="shared-scratch" path="/scratch/00384/rynge/workflow-runs">
<file-server operation="all" url="file:///scratch/00384/rynge/workflow-runs"/>
</directory>
<directory type="local-storage" path="/work/00384/rynge/workflow-outputs">
<file-server operation="all" url="file:///work/00384/rynge/workflow-outputs"/>
</directory>

With the new leaf cleanup code, I get:

2014.03.10 11:50:28.570 PDT: [FATAL ERROR] java.lang.NullPointerException
at edu.isi.pegasus.planner.refiner.RemoveDirectory.makeRemoveDirJob(RemoveDirectory.java:445)
at edu.isi.pegasus.planner.refiner.RemoveDirectory.makeRemoveDirJob(RemoveDirectory.java:419)
at edu.isi.pegasus.planner.refiner.RemoveDirectory.addRemoveDirectoryNodes(RemoveDirectory.java:263)
at edu.isi.pegasus.planner.refiner.RemoveDirectory.addRemoveDirectoryNodes(RemoveDirectory.java:204)
at edu.isi.pegasus.planner.refiner.MainEngine.runPlanner(MainEngine.java:276)
at edu.isi.pegasus.planner.client.CPlanner.executeCommand(CPlanner.java:646)
at edu.isi.pegasus.planner.client.CPlanner.executeCommand(CPlanner.java:366)
at edu.isi.pegasus.planner.client.CPlanner.main(CPlanner.java:254)