Looking through the documentation, I could not find any mention of the
coverage of the application versions.

Experience and my gut tells me that these components are not versioned:
* Database Indexes and the persistence layers
war/WEB-INF/appengine-generated/datastore-indexes.xml
war/WEB-INF/appengine-generated/datastore-indexes-auto.xml

* crontab
war/WEB-INF/cron.xml

* task queues
war/WEB-INF/queue.xml

* Dos entries
war/WEB-INF/dos.xml
-------------------------

Is the web.xml versioned?
war/WEB-INF/web.xml

Is the logging.properties versioned?
war/WEB-INF/logging.properties

Are static files (html, css, images, jsp, swf, etc)  versioned?

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