let Galaxy use output_to_working dir

most importantly this will set the galaxy dir and its files dir
to read only. which allows planemo test to find cases of tools
that write into galaxy's files dir.

see also here https://github.com/galaxyproject/galaxy/blob/5dc9111f45b4ed5012575b31e199a591cfad6d7a/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L483

planemo/galaxy/config.py

@@ -493,6 +493,7 @@ def config_join(*args):
             migrated_tools_config=empty_tool_conf,
             test_data_dir=test_data_dir,  # TODO: make gx respect this
             shed_data_manager_config_file=shed_data_manager_config_file,
+            outputs_to_working_directory = "True",
         ))
         _handle_container_resolution(ctx, kwds, properties)
         write_file(config_join("logging.ini"), _sub(LOGGING_TEMPLATE, template_args))