I installed the app-schema JARs and the tutorial data directory on a local GeoServer 2.12.2 instance.
Doing (an abbreviated version of) the demo query from http://docs.geoserver.org/latest/en/user/data/app-schema/tutorial.html#installation results in a broken document:
Note missing xlink namespace on href attribute of gsml:specification, and missing xmlns:xlink namespace prefix declaration on the root element.
I actually ran into this issue with a custom schema. A proximate cause for missing namespace prefix declaration seems to be that the namespace prefixes declared in AppSchemaDataAccess/namespaces are never added to the XSD Schema when the Encoder is created in GML3OutputFormat.