User interface to permissions, and a bunch of changes to ensure that

both permitted_actions and groups are set appropriately on datasets.
Somewhat tested and mostly working, but needs more testing.

Greg: If a userless session has a history, if that user logs in,
the DefaultHistoryGroupAssociation for the current history as well
as the datasets in that history are supposed to be updated with the
permissions in DefaultUserGroupAssociation, but this isn't happening.
Possibly because the default permissions on userless histories create
datasets in the public group with only the DATASET_ACCESS permission
(or possibly for another reason).  What are the implications of giving
public users DATASET_MANAGE_PERMISSIONS?

tools/data_source/encode_import_code.py

@@ -38,8 +38,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             newdata.extension = file_type
             newdata.name = basic_name + " (" + description + ")"
             history.add_dataset( newdata )
-            #TODO, Nate: Make sure the following is functionally correct
-            app.security_agent.set_dataset_groups( newdata.dataset, base_dataset.dataset.groups )
+            app.security_agent.set_dataset_permissions( newdata.dataset, base_dataset.dataset.groups )
             app.model.flush()
             try:
                 copyfile(filepath,newdata.file_name)