Issue #2886622 by Berdir, martin107, Mile23, tim.plunkett, mikelutz, jonathan1055: Deprecate all EntityManager methods with E_USER_DEPRECATED

Issue #2665992 by alexpott, klausi, heykarthikwithu, xjm, tstoeckler: @file is not required for classes, interfaces and traits

Issue #1392754 by tss, justAChris, jhodgdon: Comply with new documentation standards for @file for namespaced class files