Flatten the deep dir structure in atenet

I just noticed that the directory structure is pretty deep. I want to
make this less deep before we get too far into the project:

* cmd/atenet/internal/app << this directory level is not needed. get rid of it.
* cmd/atenet/internal/router/* move everything but the cobra flags to internal/router
* cmd/atenet/internal/* just has the cobra flags definitions

This is moving files -- no logic change.

.golangci.yaml

@@ -100,12 +100,6 @@ linters:
       # json.Encoder.Encode in HTTP-handler write paths is fire-and-forget.
       - linters: [errcheck]
         text: 'Error return value of `\(\*encoding/json\.Encoder\)\.Encode` is not checked'
-      # ST1019: duplicate import aliases in extproc_out.go are pending a
-      # separate cleanup that will collide with an in-flight PR; suppress
-      # in this file for now.
-      - path: '^cmd/atenet/internal/app/router/extproc_out\.go$'
-        linters: [staticcheck]
-        text: '^ST1019'
 
 issues:
   max-issues-per-linter: 0

cmd/atenet/internal/dns.go

@@ -12,7 +12,7 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-package dns
+package internal
 
 import (
 	"context"
@@ -24,11 +24,12 @@ import (
 	"syscall"
 	"time"
 
-	"github.com/agent-substrate/substrate/internal/dns"
 	"github.com/spf13/cobra"
 	"k8s.io/client-go/tools/clientcmd"
 	"sigs.k8s.io/controller-runtime/pkg/client"
 	"sigs.k8s.io/controller-runtime/pkg/client/config"
+
+	"github.com/agent-substrate/substrate/internal/dns"
 )
 
 type DnsConfig struct {
@@ -38,7 +39,7 @@ type DnsConfig struct {
 	CorefilePath      string
 }
 
-func NewCmd() *cobra.Command {
+func NewDnsCmd() *cobra.Command {
 	var cfg DnsConfig
 
 	cmd := &cobra.Command{

cmd/atenet/internal/root.go

@@ -12,14 +12,12 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-package app
+package internal
 
 import (
 	"fmt"
 	"os"
 
-	"github.com/agent-substrate/substrate/cmd/atenet/internal/app/dns"
-	"github.com/agent-substrate/substrate/cmd/atenet/internal/app/router"
 	"github.com/agent-substrate/substrate/internal/version"
 	"github.com/spf13/cobra"
 )
@@ -39,6 +37,6 @@ func Execute() {
 }
 
 func init() {
-	rootCmd.AddCommand(router.NewCmd())
-	rootCmd.AddCommand(dns.NewCmd())
+	rootCmd.AddCommand(NewRouterCmd())
+	rootCmd.AddCommand(NewDnsCmd())
 }

cmd/atenet/internal/router.go

@@ -0,0 +1,61 @@
+// Copyright 2026 Google LLC
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package internal
+
+import (
+	"fmt"
+	"time"
+
+	"github.com/spf13/cobra"
+
+	"github.com/agent-substrate/substrate/internal/router"
+)
+
+func NewRouterCmd() *cobra.Command {
+	var cfg router.RouterConfig
+
+	cmd := &cobra.Command{
+		Use:   "router",
+		Short: "Router components including xDS server and Envoy ExtProc gateway processing server",
+		RunE: func(cmd *cobra.Command, args []string) error {
+			srv, err := router.NewRouterServer(cfg)
+			if err != nil {
+				return fmt.Errorf("failed to create router server: %w", err)
+			}
+			srv.Cmd = cmd
+
+			return srv.Run(cmd.Context())
+		},
+	}
+
+	cmd.Flags().StringVar(&cfg.LogLevel, "log-level", "info", "Log level: debug, info, warn, error")
+	cmd.Flags().StringVar(&cfg.MetricsAddr, "metrics-listen-addr", ":9090", "Address and port the prometheus metrics server should listen on.")
+	cmd.Flags().BoolVar(&cfg.Standalone, "standalone", false, "Run in standalone mode, bypassing creation of managed deployment and services in Kubernetes cluster")
+	cmd.Flags().StringVar(&cfg.Namespace, "namespace", "default", "Target operations namespace")
+	cmd.Flags().StringVar(&cfg.Kubeconfig, "kubeconfig", "", "Absolute path to the kubeconfig configuration file")
+	cmd.Flags().StringVar(&cfg.AteapiAddr, "ateapi-address", "api.ate-system.svc:443", "gRPC host address of the cluster ateapi Control instance")
+	cmd.Flags().IntVar(&cfg.HttpPort, "port-http", 8080, "TCP port for workload traffic entering through the Envoy Router")
+	cmd.Flags().IntVar(&cfg.XdsPort, "port-xds", 18000, "TCP port listening for the xDS dynamic Envoy connections")
+	cmd.Flags().IntVar(&cfg.ExtprocPort, "port-extproc", 50051, "Listen port for the Envoy dynamic External Processing (ext_proc) server")
+	cmd.Flags().StringVar(&cfg.ExtprocAddr, "extproc-address", "127.0.0.1", "Host IP or address of the Envoy External Processing (ext_proc) server")
+	cmd.Flags().StringVar(&cfg.EnvoyImage, "envoy-image", "envoyproxy/envoy:v1.30-latest", "Image URI used for dynamically launched router instances")
+	cmd.Flags().StringVar(&cfg.TemplatesFile, "actor-templates-file", "", "Path to offline YAML configuration file listing ActorTemplates")
+	cmd.Flags().IntVar(&cfg.StatusPort, "status-port", 4040, "Port to serve /statusz on (set <= 0 to disable serving status)")
+	cmd.Flags().DurationVar(&cfg.HealthInterval, "health-interval", 1*time.Second, "Interval for checking health of dependent services")
+	cmd.Flags().IntVar(&cfg.HttpsPort, "port-https", 8443, "TCP port for HTTPS workload traffic entering through the Envoy Router")
+	cmd.Flags().StringVar(&cfg.EnvoyCertPath, "envoy-cert-path", "", "Path to the Envoy certificate file (if empty, a self-signed cert will be generated for testing)")
+
+	return cmd
+}

cmd/atenet/main.go

@@ -14,8 +14,8 @@
 
 package main
 
-import "github.com/agent-substrate/substrate/cmd/atenet/internal/app"
+import "github.com/agent-substrate/substrate/cmd/atenet/internal"
 
 func main() {
-	app.Execute()
+	internal.Execute()
 }

internal/router/extproc_out.go

@@ -17,7 +17,6 @@ package router
 import (
 	corev3 "github.com/envoyproxy/go-control-plane/envoy/config/core/v3"
 	extproc "github.com/envoyproxy/go-control-plane/envoy/service/ext_proc/v3"
-	extprocv3 "github.com/envoyproxy/go-control-plane/envoy/service/ext_proc/v3"
 	envoy_type "github.com/envoyproxy/go-control-plane/envoy/type/v3"
 )
 
@@ -33,7 +32,7 @@ type reqError struct {
 func (e *reqError) Error() string { return e.msg }
 func (e *reqError) Unwrap() error { return e.cause }
 
-func addAuthorityMutation(auth string, mut *extprocv3.HeaderMutation) {
+func addAuthorityMutation(auth string, mut *extproc.HeaderMutation) {
 	mut.SetHeaders = append(mut.SetHeaders,
 		&corev3.HeaderValueOption{
 			Header: &corev3.HeaderValue{

internal/router/router.go

@@ -84,7 +84,7 @@ type RouterConfig struct {
 type RouterServer struct {
 	cfg RouterConfig
 
-	cmd        *cobra.Command
+	Cmd        *cobra.Command
 	k8sClient  client.Client
 	clientset  kubernetes.Interface
 	apiClient  ateapipb.ControlClient
@@ -93,74 +93,6 @@ type RouterServer struct {
 	atStore    atStore
 }
 
-func NewCmd() *cobra.Command {
-	var cfg RouterConfig
-
-	cmd := &cobra.Command{
-		Use:   "router",
-		Short: "Router components including xDS server and Envoy ExtProc gateway processing server",
-		RunE: func(cmd *cobra.Command, args []string) error {
-			ctx, cancel := context.WithCancel(cmd.Context())
-			defer cancel()
-
-			var level slog.Level
-			switch strings.ToLower(cfg.LogLevel) {
-			case "debug":
-				level = slog.LevelDebug
-			case "warn":
-				level = slog.LevelWarn
-			case "error":
-				level = slog.LevelError
-			default:
-				level = slog.LevelInfo
-			}
-			slog.SetDefault(slog.New(slog.NewJSONHandler(os.Stdout, &slog.HandlerOptions{Level: level})))
-
-			mp, err := serverboot.InitMetrics(ctx, routerServiceName)
-			if err != nil {
-				return fmt.Errorf("failed to initialize metrics: %w", err)
-			}
-			defer serverboot.ShutdownProvider("MeterProvider", mp.Shutdown)
-
-			go serverboot.StartMetricsServer(ctx, serverboot.MetricsServerOptions{Addr: cfg.MetricsAddr})
-
-			sigChan := make(chan os.Signal, 1)
-			signal.Notify(sigChan, syscall.SIGINT, syscall.SIGTERM)
-			go func() {
-				<-sigChan
-				cancel()
-			}()
-
-			srv, err := NewRouterServer(cfg)
-			if err != nil {
-				return fmt.Errorf("failed to create router server: %w", err)
-			}
-			srv.cmd = cmd
-
-			return srv.Run(ctx)
-		},
-	}
-
-	cmd.Flags().StringVar(&cfg.LogLevel, "log-level", "info", "Log level: debug, info, warn, error")
-	cmd.Flags().StringVar(&cfg.MetricsAddr, "metrics-listen-addr", ":9090", "Address and port the prometheus metrics server should listen on.")
-	cmd.Flags().BoolVar(&cfg.Standalone, "standalone", false, "Run in standalone mode, bypassing creation of managed deployment and services in Kubernetes cluster")
-	cmd.Flags().StringVar(&cfg.Namespace, "namespace", "default", "Target operations namespace")
-	cmd.Flags().StringVar(&cfg.Kubeconfig, "kubeconfig", "", "Absolute path to the kubeconfig configuration file")
-	cmd.Flags().StringVar(&cfg.AteapiAddr, "ateapi-address", "api.ate-system.svc:443", "gRPC host address of the cluster ateapi Control instance")
-	cmd.Flags().IntVar(&cfg.HttpPort, "port-http", 8080, "TCP port for workload traffic entering through the Envoy Router")
-	cmd.Flags().IntVar(&cfg.XdsPort, "port-xds", 18000, "TCP port listening for the xDS dynamic Envoy connections")
-	cmd.Flags().IntVar(&cfg.ExtprocPort, "port-extproc", 50051, "Listen port for the Envoy dynamic External Processing (ext_proc) server")
-	cmd.Flags().StringVar(&cfg.ExtprocAddr, "extproc-address", "127.0.0.1", "Host IP or address of the Envoy External Processing (ext_proc) server")
-	cmd.Flags().StringVar(&cfg.EnvoyImage, "envoy-image", "envoyproxy/envoy:v1.30-latest", "Image URI used for dynamically launched router instances")
-	cmd.Flags().StringVar(&cfg.TemplatesFile, "actor-templates-file", "", "Path to offline YAML configuration file listing ActorTemplates")
-	cmd.Flags().IntVar(&cfg.StatusPort, "status-port", 4040, "Port to serve /statusz on (set <= 0 to disable serving status)")
-	cmd.Flags().DurationVar(&cfg.HealthInterval, "health-interval", 1*time.Second, "Interval for checking health of dependent services")
-	cmd.Flags().IntVar(&cfg.HttpsPort, "port-https", 8443, "TCP port for HTTPS workload traffic entering through the Envoy Router")
-	cmd.Flags().StringVar(&cfg.EnvoyCertPath, "envoy-cert-path", "", "Path to the Envoy certificate file (if empty, a self-signed cert will be generated for testing)")
-
-	return cmd
-}
-
 func NewRouterServer(cfg RouterConfig) (*RouterServer, error) {
 	var k8sClient client.Client
 	var clientset kubernetes.Interface
@@ -218,6 +150,37 @@ func NewRouterServer(cfg RouterConfig) (*RouterServer, error) {
 }
 
 func (s *RouterServer) Run(ctx context.Context) error {
+	ctx, cancel := context.WithCancel(ctx)
+	defer cancel()
+
+	sigChan := make(chan os.Signal, 1)
+	signal.Notify(sigChan, syscall.SIGINT, syscall.SIGTERM)
+	go func() {
+		<-sigChan
+		cancel()
+	}()
+
+	var level slog.Level
+	switch strings.ToLower(s.cfg.LogLevel) {
+	case "debug":
+		level = slog.LevelDebug
+	case "warn":
+		level = slog.LevelWarn
+	case "error":
+		level = slog.LevelError
+	default:
+		level = slog.LevelInfo
+	}
+	slog.SetDefault(slog.New(slog.NewJSONHandler(os.Stdout, &slog.HandlerOptions{Level: level})))
+
+	mp, err := serverboot.InitMetrics(ctx, routerServiceName)
+	if err != nil {
+		return fmt.Errorf("failed to initialize metrics: %w", err)
+	}
+	defer serverboot.ShutdownProvider("MeterProvider", mp.Shutdown)
+
+	go serverboot.StartMetricsServer(ctx, serverboot.MetricsServerOptions{Addr: s.cfg.MetricsAddr})
+
 	slog.InfoContext(ctx, "Starting substrate router subsystem", slog.Bool("standalone", s.cfg.Standalone))
 
 	g, ctx := errgroup.WithContext(ctx)

internal/router/status.go

@@ -188,8 +188,8 @@ func (s *RouterServer) handleStatusz(w http.ResponseWriter, req *http.Request) {
 	argsStr := strings.Join(os.Args, " ")
 
 	flagsMap := make(map[string]string)
-	if s.cmd != nil {
-		s.cmd.Flags().VisitAll(func(f *pflag.Flag) {
+	if s.Cmd != nil {
+		s.Cmd.Flags().VisitAll(func(f *pflag.Flag) {
 			flagsMap[f.Name] = f.Value.String()
 		})
 	}