Updated all consolidated application definitions for apm and em. Some base...

Updated all consolidated application definitions for apm and em. Some base class names were changed to reflect better their changed usage and intention: NXstage became NXstage_lab to reflect that modern stages are labs on the stage and enable building of stage/holder device/component hierarchies, NXdeflector became NXlens_apm to reflect the specific case of reflectrons, NXem_snbdiff was removed for the reason of deprecation, NXem is now meant only to be used as template/inspiration for starting the building of case-specific application definitions for em: two examples of such were given: NXem_nion (for Nion microscopes joint by Christophs group), NXem_edxs (a generic STEM experiment case with X-ray spectroscopy joint by EPFL)