Move nginx config and cert generation to box code

src/server.js

@@ -270,6 +270,7 @@ function start(callback) {
         auth.initialize,
         database.initialize,
         cloudron.initialize, // keep this here because it reads activation state that others depend on
+        certificates.initialize,
         certificates.installAdminCertificate, // keep this before cron to block heartbeats until cert is ready
         platform.initialize,
         taskmanager.initialize,