Many changes to get initialization working properly with the new setup page.

...java/org/nrg/xapi/exceptions/InitializationException.java

src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java

...in/java/org/nrg/xnat/configuration/ApplicationConfig.java

src/main/java/org/nrg/xnat/initialization/RootConfig.java

src/main/java/org/nrg/xnat/security/XnatInitCheckFilter.java

src/main/java/org/nrg/xnat/services/XnatAppInfo.java

...a/org/nrg/xnat/turbine/modules/screens/Configuration.java

...va/org/nrg/xnat/turbine/modules/screens/EditArcSpecs.java

src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java

src/main/webapp/WEB-INF/conf/xnat-security.xml

src/main/webapp/page/admin/data/config/site-setup.yaml

src/main/webapp/xnat-templates/screens/Configuration.vm

src/main/webapp/xnat-templates/screens/EditArcSpecs.vm

...app/xnat-templates/screens/configuration/anonymization.vm

...in/webapp/xnat-templates/screens/configuration/applets.vm

...app/xnat-templates/screens/configuration/dicomReceiver.vm

...n/webapp/xnat-templates/screens/configuration/features.vm

...webapp/xnat-templates/screens/configuration/fileSystem.vm

...pp/xnat-templates/screens/configuration/mockRestConfig.vm

...app/xnat-templates/screens/configuration/notifications.vm