diff --git a/internal/cmd/config.go b/internal/cmd/config.go
index 23edc4b..a05ee24 100644
--- a/internal/cmd/config.go
+++ b/internal/cmd/config.go
@@ -19,11 +19,11 @@ import (
 var configCmd = &cobra.Command{
 	Use:   "config",
 	Short: "View and manage CLI and workspace configuration",
-	Long: `mol config list      — list all config keys (from file + env)
-mol config get <key> — print a single config value
-mol config set <key> <value> — write a key to the config file
-mol config init      — scaffold a default mol.yaml in the current directory
-mol config view      — print the current config file with sources annotated`,
+	Long: `molecule config list      — list all config keys (from file + env)
+molecule config get <key> — print a single config value
+molecule config set <key> <value> — write a key to the config file
+molecule config init      — scaffold a default molecule.yaml in the current directory
+molecule config view      — print the current config file with sources annotated`,
 }
 
 func init() {
@@ -44,7 +44,7 @@ var configListCmd = &cobra.Command{
 func runConfigList(cmd *cobra.Command, _ []string) error {
 	settings := viper.AllSettings()
 	if len(settings) == 0 {
-		fmt.Println("No config keys set. Use `mol config set <key> <value>` or set env vars.")
+		fmt.Println("No config keys set. Use `molecule config set <key> <value>` or set env vars.")
 		return nil
 	}
 	w := tabwriter.NewWriter(os.Stdout, 0, 4, 2, ' ', 0)
@@ -85,7 +85,7 @@ func runConfigGet(cmd *cobra.Command, args []string) error {
 // ===========================================================================
 var configSetCmd = &cobra.Command{
 	Use:   "set <key> <value>",
-	Short: "Write a config key to the config file (~/.config/mol.yaml)",
+	Short: "Write a config key to the config file (~/.config/molecule.yaml)",
 	Args:  cobra.ExactArgs(2),
 	RunE:  runConfigSet,
 }
@@ -96,7 +96,7 @@ func runConfigSet(cmd *cobra.Command, args []string) error {
 	if err != nil {
 		configDir = "."
 	}
-	configFile := filepath.Join(configDir, "mol.yaml")
+	configFile := filepath.Join(configDir, "molecule.yaml")
 
 	v := viper.New()
 	v.SetConfigFile(configFile)
@@ -116,12 +116,12 @@ func runConfigSet(cmd *cobra.Command, args []string) error {
 // ===========================================================================
 var configInitCmd = &cobra.Command{
 	Use:   "init",
-	Short: "Scaffold a default mol.yaml in the current directory",
+	Short: "Scaffold a default molecule.yaml in the current directory",
 	RunE:  runConfigInit,
 }
 
 func runConfigInit(cmd *cobra.Command, _ []string) error {
-	const defaultConfig = `# mol CLI config — https://github.com/Molecule-AI/molecule-cli
+	const defaultConfig = `# molecule CLI config — https://github.com/Molecule-AI/molecule-cli
 #
 # All values can be overridden by environment variables:
 #   MOLECULE_API_URL, MOLECULE_RUNTIME_URL, MOL_OUTPUT, MOL_VERBOSE, etc.
@@ -135,13 +135,13 @@ func runConfigInit(cmd *cobra.Command, _ []string) error {
 # Verbose logging: true | false  (env: MOL_VERBOSE)
 # verbose: false
 `
-	if _, err := os.Stat("mol.yaml"); err == nil {
-		return fmt.Errorf("config init: mol.yaml already exists (not overwriting)")
+	if _, err := os.Stat("molecule.yaml"); err == nil {
+		return fmt.Errorf("config init: molecule.yaml already exists (not overwriting)")
 	}
-	if err := os.WriteFile("mol.yaml", []byte(defaultConfig), 0o644); err != nil {
-		return fmt.Errorf("config init: write mol.yaml: %w", err)
+	if err := os.WriteFile("molecule.yaml", []byte(defaultConfig), 0o644); err != nil {
+		return fmt.Errorf("config init: write molecule.yaml: %w", err)
 	}
-	fmt.Println("Scaffolded mol.yaml — edit it and run mol --config mol.yaml, or move it to ~/.config/mol.yaml")
+	fmt.Println("Scaffolded molecule.yaml — edit it and run molecule --config molecule.yaml, or move it to ~/.config/molecule.yaml")
 	return nil
 }
 
@@ -156,7 +156,7 @@ var configViewCmd = &cobra.Command{
 
 func runConfigView(cmd *cobra.Command, _ []string) error {
 	if viper.ConfigFileUsed() == "" {
-		fmt.Println("No config file in use. Set one with --config or mol config init.")
+		fmt.Println("No config file in use. Set one with --config or molecule config init.")
 		fmt.Println("\nActive env vars starting with MOLECULE_ or MOL_:")
 		for _, env := range os.Environ() {
 			if strings.HasPrefix(env, "MOLECULE_") || strings.HasPrefix(env, "MOL_") {
diff --git a/internal/cmd/root.go b/internal/cmd/root.go
index 0988d4c..35f04e4 100644
--- a/internal/cmd/root.go
+++ b/internal/cmd/root.go
@@ -25,18 +25,18 @@ var (
 
 // rootCmd is the top-level molecule command.
 var rootCmd = &cobra.Command{
-	Use:     "mol",
+	Use:     "molecule",
 	Version: Version,
-	Short:   "mol — Molecule AI platform CLI",
-	Long: `mol is the CLI for the Molecule AI agent platform.
+	Short:   "molecule — Molecule AI platform CLI",
+	Long: `molecule is the CLI for the Molecule AI agent platform.
 
 Manage workspaces, inspect agents, audit the platform, and configure
 agent behaviour from the terminal.
 
 Quick start:
-  mol workspace list
-  mol agent list
-  mol platform health`,
+  molecule workspace list
+  molecule agent list
+  molecule platform health`,
 	SilenceUsage:   true,
 	SilenceErrors:  true,
 }
@@ -50,7 +50,7 @@ func init() {
 	rootCmd.PersistentFlags().StringVarP(&outputFormat, "output", "o", "table",
 		"Output format: table | json | yaml")
 	rootCmd.PersistentFlags().StringVar(&configPath, "config", "",
-		"Path to config file (default ~/.config/mol.yaml or ./mol.yaml)")
+		"Path to config file (default ~/.config/molecule.yaml or ./molecule.yaml)")
 	rootCmd.SetFlagErrorFunc(func(cmd *cobra.Command, err error) error {
 		return &exitError{code: 2, msg: err.Error()}
 	})
@@ -63,7 +63,7 @@ func Execute() error {
 	if configPath != "" {
 		viper.SetConfigFile(configPath)
 	} else {
-		viper.SetConfigName("mol")
+		viper.SetConfigName("molecule")
 		viper.AddConfigPath("$HOME/.config")
 		viper.AddConfigPath(".")
 	}
@@ -87,6 +87,7 @@ func init() {
 	rootCmd.AddCommand(agentCmd)
 	rootCmd.AddCommand(platformCmd)
 	rootCmd.AddCommand(configCmd)
+	rootCmd.AddCommand(initCmd)
 }
 
 // exitError wraps a user-facing error with a specific exit code.
@@ -122,5 +123,5 @@ func kv(w *tabwriter.Writer, k, v string) {
 }
 
 func versionInfo() string {
-	return fmt.Sprintf("mol %s (go %s)", Version, runtime.Version())
+	return fmt.Sprintf("molecule %s (go %s)", Version, runtime.Version())
 }
\ No newline at end of file