I got similar exception. In my case, I just added new entity class and forgot to annotate it with @Entity. And stacktrace looked like:
java.lang.ExceptionInInitializerError
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:274)
at com.google.api.server.spi.ServletInitializationParameters.getClassForName(ServletInitializationParameters.java:82)
...
Caused by: java.lang.IllegalArgumentException: class com.myapp.entity.Stat must be annotated with either @Entity or @Subclass
at com.googlecode.objectify.impl.Registrar.register(Registrar.java:81)
at com.googlecode.objectify.ObjectifyFactory.register(ObjectifyFactory.java:185)
at com.googlecode.objectify.ObjectifyService.register(ObjectifyService.java:64)
...
Jun 18, 2016 7:13:39 PM com.google.apphosting.utils.jetty.JettyLogger warn
WARNING: /_ah/api/discovery/v1/apis/userapi/v1/rest: java.io.IOException:
Failed to retrieve API configs with status: 500
Jun 18, 2016 7:13:39 PM com.google.apphosting.utils.jetty.JettyLogger warn
WARNING: /_ah/spi/BackendService.getApiConfigs
java.lang.NullPointerException
at com.google.api.server.spi.SystemServiceServlet.
After I added annotation to class, exception is gone.