fix: bind CLI config file values to cobra flags

go/core/cli/cmd/kagent/main.go

@@ -429,12 +429,29 @@ Examples:
 
 	rootCmd.AddCommand(installCmd, uninstallCmd, invokeCmd, bugReportCmd, versionCmd, dashboardCmd, getCmd, initCmd, buildCmd, deployCmd, addMcpCmd, runCmd, mcp.NewMCPCmd(), envdoc.NewEnvCmd())
 
-	// Initialize config
+	// Initialize config file and viper defaults
 	if err := config.Init(); err != nil {
 		fmt.Fprintf(os.Stderr, "Error initializing config: %v\n", err)
 		os.Exit(1)
 	}
 
+	// Bind cobra flags to viper so config file values are used when flags
+	// are not explicitly set on the command line.
+	config.BindFlags(rootCmd.PersistentFlags())
+
+	// Populate cfg from the merged viper state (config file + env + flags)
+	// before any subcommand runs, ensuring all commands see config file values.
+	originalPreRunE := rootCmd.PersistentPreRunE
+	rootCmd.PersistentPreRunE = func(cmd *cobra.Command, args []string) error {
+		if err := config.Apply(cfg); err != nil {
+			return fmt.Errorf("error applying config: %w", err)
+		}
+		if originalPreRunE != nil {
+			return originalPreRunE(cmd, args)
+		}
+		return nil
+	}
+
 	if err := rootCmd.ExecuteContext(ctx); err != nil {
 		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
 

go/core/cli/internal/config/config.go

@@ -62,6 +62,30 @@ func Init() error {
 	return nil
 }
 
+// BindFlags binds cobra persistent flags to viper keys so that config file
+// values are used as defaults when the corresponding CLI flag is not explicitly
+// set. Flag names use dashes (e.g. "kagent-url") while config file keys use
+// underscores (e.g. "kagent_url"), so each binding is explicit.
+func BindFlags(flags *pflag.FlagSet) {
+	viper.BindPFlag("kagent_url", flags.Lookup("kagent-url"))     //nolint:errcheck
+	viper.BindPFlag("namespace", flags.Lookup("namespace"))        //nolint:errcheck
+	viper.BindPFlag("output_format", flags.Lookup("output-format")) //nolint:errcheck
+	viper.BindPFlag("verbose", flags.Lookup("verbose"))            //nolint:errcheck
+	viper.BindPFlag("timeout", flags.Lookup("timeout"))            //nolint:errcheck
+}
+
+// Apply populates the given Config from the merged viper state (config file +
+// env + CLI flags). Call this after flag parsing to ensure cfg reflects all
+// sources with the correct precedence: CLI flag > env > config file > default.
+func Apply(cfg *Config) error {
+	merged, err := Get()
+	if err != nil {
+		return err
+	}
+	*cfg = *merged
+	return nil
+}
+
 func Get() (*Config, error) {
 	var config Config
 	if err := viper.Unmarshal(&config); err != nil {

go/core/cli/internal/config/config_test.go

@@ -0,0 +1,133 @@
+package config
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/spf13/pflag"
+	"github.com/spf13/viper"
+)
+
+func TestConfigFileValuesAreUsed(t *testing.T) {
+	// Reset viper for a clean test
+	viper.Reset()
+
+	// Create a temp config directory
+	tmpDir := t.TempDir()
+	configFile := filepath.Join(tmpDir, "config.yaml")
+
+	// Write a config file with custom values
+	configContent := `kagent_url: http://custom-server:9090
+namespace: my-namespace
+output_format: json
+verbose: true
+timeout: 60s
+`
+	if err := os.WriteFile(configFile, []byte(configContent), 0644); err != nil {
+		t.Fatalf("Failed to write config file: %v", err)
+	}
+
+	// Set up viper to read the config
+	viper.SetConfigFile(configFile)
+	viper.SetConfigType("yaml")
+	viper.SetDefault("kagent_url", "http://localhost:8083")
+	viper.SetDefault("output_format", "table")
+	viper.SetDefault("namespace", "kagent")
+	viper.SetDefault("timeout", 300*time.Second)
+
+	if err := viper.ReadInConfig(); err != nil {
+		t.Fatalf("Failed to read config: %v", err)
+	}
+
+	// Create flags (simulating what main.go does)
+	flags := pflag.NewFlagSet("test", pflag.ContinueOnError)
+	flags.String("kagent-url", "http://localhost:8083", "KAgent URL")
+	flags.StringP("namespace", "n", "kagent", "Namespace")
+	flags.StringP("output-format", "o", "table", "Output format")
+	flags.BoolP("verbose", "v", false, "Verbose output")
+	flags.Duration("timeout", 300*time.Second, "Timeout")
+
+	// Bind flags to viper
+	BindFlags(flags)
+
+	// Get merged config (should use config file values since no flags were explicitly set)
+	cfg := &Config{}
+	if err := Apply(cfg); err != nil {
+		t.Fatalf("Apply failed: %v", err)
+	}
+
+	if cfg.KAgentURL != "http://custom-server:9090" {
+		t.Errorf("Expected KAgentURL=http://custom-server:9090, got %s", cfg.KAgentURL)
+	}
+	if cfg.Namespace != "my-namespace" {
+		t.Errorf("Expected Namespace=my-namespace, got %s", cfg.Namespace)
+	}
+	if cfg.OutputFormat != "json" {
+		t.Errorf("Expected OutputFormat=json, got %s", cfg.OutputFormat)
+	}
+	if !cfg.Verbose {
+		t.Error("Expected Verbose=true, got false")
+	}
+	if cfg.Timeout != 60*time.Second {
+		t.Errorf("Expected Timeout=60s, got %v", cfg.Timeout)
+	}
+}
+
+func TestCLIFlagsOverrideConfigFile(t *testing.T) {
+	// Reset viper for a clean test
+	viper.Reset()
+
+	// Create a temp config directory
+	tmpDir := t.TempDir()
+	configFile := filepath.Join(tmpDir, "config.yaml")
+
+	// Write a config file with custom values
+	configContent := `kagent_url: http://config-server:9090
+namespace: config-ns
+`
+	if err := os.WriteFile(configFile, []byte(configContent), 0644); err != nil {
+		t.Fatalf("Failed to write config file: %v", err)
+	}
+
+	viper.SetConfigFile(configFile)
+	viper.SetConfigType("yaml")
+	viper.SetDefault("kagent_url", "http://localhost:8083")
+	viper.SetDefault("namespace", "kagent")
+	viper.SetDefault("output_format", "table")
+	viper.SetDefault("timeout", 300*time.Second)
+
+	if err := viper.ReadInConfig(); err != nil {
+		t.Fatalf("Failed to read config: %v", err)
+	}
+
+	// Create and parse flags with explicit values
+	flags := pflag.NewFlagSet("test", pflag.ContinueOnError)
+	flags.String("kagent-url", "http://localhost:8083", "KAgent URL")
+	flags.StringP("namespace", "n", "kagent", "Namespace")
+	flags.StringP("output-format", "o", "table", "Output format")
+	flags.BoolP("verbose", "v", false, "Verbose output")
+	flags.Duration("timeout", 300*time.Second, "Timeout")
+
+	// Simulate passing --kagent-url on the CLI
+	if err := flags.Parse([]string{"--kagent-url", "http://cli-override:7777"}); err != nil {
+		t.Fatalf("Failed to parse flags: %v", err)
+	}
+
+	BindFlags(flags)
+
+	cfg := &Config{}
+	if err := Apply(cfg); err != nil {
+		t.Fatalf("Apply failed: %v", err)
+	}
+
+	// CLI flag should win over config file
+	if cfg.KAgentURL != "http://cli-override:7777" {
+		t.Errorf("Expected KAgentURL=http://cli-override:7777, got %s", cfg.KAgentURL)
+	}
+	// Config file value should still be used for namespace (not overridden by CLI)
+	if cfg.Namespace != "config-ns" {
+		t.Errorf("Expected Namespace=config-ns, got %s", cfg.Namespace)
+	}
+}