ModuleService: add more run method signatures

This change is in preparation for the migration of some
non-command-specific run methods out of CommandService.

It also deprecates some previous signatures since they would become
ambiguous with respect to whether pre- and postprocessing should occur.
CommandService: improve the run method signatures

The non-command-specific signatures have been deprecated, having
migrated to the ModuleService. Every run signature also now takes a
"boolean process" flag for specifying whether pre- and postprocessing
should be done; previously, the CommandService *always* did pre- and
postprocessing.