While doing a clean bootstrap of the current trunk I get the following warning, although I am not updating an older version:

WARN info.magnolia.module.InstallContextImpl.warn(InstallContextImpl.java:53) > CacheGeneratorServlet has been removed in Magnolia 3.1: please remove the corresponding <servlet> and <servlet-mapping> elements in your web.xml file.
WARN info.magnolia.module.InstallContextImpl.warn(InstallContextImpl.java:53) > MagnoliaManagedFilter was renamed to MagnoliaMainFilter: please update the corresponding <filter-class> element in your web.xml file.

Those are now unconditionally added in info.magnolia.setup.CoreModuleVersionHandler, instead the in the deprecated classes as before. They should be conditional