Unify WorkflowModule execute method across tool and input modules.

Previously tool module class did not contain this method (though it was abstract in the base class) and extra logic for dealing with tools was located outside of the module itself. Moving everything into the module (made possible by previously committed WorkflowProgress class and attaching some properties to workflow invocations and sending them in) means that now the worklfow invocation logic can uniformly deal with modules and doesn't need to dispatch on type. This should allow extending the capabilities of the workflow invoker and adding new modules independently.
API functional test for workflow 'replacement_params' and PJA renaming.