diff --git a/internal/secret/cli.go b/internal/secret/cli.go
index 6533ea8..2d91a0c 100644
--- a/internal/secret/cli.go
+++ b/internal/secret/cli.go
@@ -95,7 +95,12 @@ func getStdinScanner() *bufio.Scanner {
 // readLineFromStdin reads a single line from stdin with a prompt
 // Uses a shared scanner to avoid buffering issues between multiple calls
 func readLineFromStdin(prompt string) (string, error) {
-	fmt.Print(prompt)
+	// Check if stderr is a terminal - if not, we can't prompt interactively
+	if !term.IsTerminal(int(syscall.Stderr)) {
+		return "", fmt.Errorf("cannot prompt for input: stderr is not a terminal (running in non-interactive mode)")
+	}
+
+	fmt.Fprint(os.Stderr, prompt) // Write prompt to stderr, not stdout
 	scanner := getStdinScanner()
 	if !scanner.Scan() {
 		if err := scanner.Err(); err != nil {
@@ -108,6 +113,7 @@ func readLineFromStdin(prompt string) (string, error) {
 
 // CLIEntry is the entry point for the secret CLI application
 func CLIEntry() {
+	Debug("CLIEntry starting - debug output is working")
 	cmd := newRootCmd()
 	if err := cmd.Execute(); err != nil {
 		os.Exit(1)
@@ -115,6 +121,7 @@ func CLIEntry() {
 }
 
 func newRootCmd() *cobra.Command {
+	Debug("newRootCmd starting")
 	cmd := &cobra.Command{
 		Use:   "secret",
 		Short: "A simple secrets manager",
@@ -124,6 +131,7 @@ func newRootCmd() *cobra.Command {
 		SilenceErrors: false,
 	}
 
+	Debug("Adding subcommands to root command")
 	// Add subcommands
 	cmd.AddCommand(newInitCmd())
 	cmd.AddCommand(newGenerateCmd())
@@ -137,6 +145,7 @@ func newRootCmd() *cobra.Command {
 	cmd.AddCommand(newEncryptCmd())
 	cmd.AddCommand(newDecryptCmd())
 
+	Debug("newRootCmd completed")
 	return cmd
 }
 
@@ -280,9 +289,12 @@ func newAddCmd() *cobra.Command {
 		Long:  `Add a secret to the current vault. The secret value is read from stdin.`,
 		Args:  cobra.ExactArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
+			Debug("Add command RunE starting", "secret_name", args[0])
 			force, _ := cmd.Flags().GetBool("force")
+			Debug("Got force flag", "force", force)
 
 			cli := NewCLIInstance()
+			Debug("Created CLI instance, calling AddSecret")
 			return cli.AddSecret(args[0], force)
 		},
 	}
@@ -528,7 +540,7 @@ func (cli *CLIInstance) Init(cmd *cobra.Command) error {
 
 	// Create default vault
 	Debug("Creating default vault")
-	_, err = CreateVault(cli.fs, cli.stateDir, "default")
+	vault, err := CreateVault(cli.fs, cli.stateDir, "default")
 	if err != nil {
 		Debug("Failed to create default vault", "error", err)
 		return fmt.Errorf("failed to create default vault: %w", err)
@@ -550,6 +562,9 @@ func (cli *CLIInstance) Init(cmd *cobra.Command) error {
 		return fmt.Errorf("failed to write long-term public key: %w", err)
 	}
 
+	// Unlock the vault with the derived long-term key
+	vault.Unlock(ltIdentity)
+
 	// Prompt for passphrase for unlock key
 	var passphraseStr string
 	if envPassphrase := os.Getenv(EnvUnlockPassphrase); envPassphrase != "" {
@@ -567,7 +582,7 @@ func (cli *CLIInstance) Init(cmd *cobra.Command) error {
 
 	// Create passphrase-protected unlock key
 	Debug("Creating passphrase-protected unlock key")
-	passphraseKey, err := CreatePassphraseKey(cli.fs, cli.stateDir, passphraseStr)
+	passphraseKey, err := vault.CreatePassphraseKey(passphraseStr)
 	if err != nil {
 		Debug("Failed to create unlock key", "error", err)
 		return fmt.Errorf("failed to create unlock key: %w", err)
@@ -749,24 +764,41 @@ func (cli *CLIInstance) VaultSelect(name string) error {
 
 // AddSecret adds a secret to the vault
 func (cli *CLIInstance) AddSecret(secretName string, force bool) error {
+	Debug("CLI AddSecret starting", "secret_name", secretName, "force", force)
+
 	// Get current vault
+	Debug("Getting current vault")
 	vault, err := GetCurrentVault(cli.fs, cli.stateDir)
 	if err != nil {
+		Debug("Failed to get current vault", "error", err)
 		return err
 	}
+	Debug("Got current vault", "vault_name", vault.Name)
 
 	// Read secret value from stdin
+	Debug("Reading secret value from stdin")
 	value, err := io.ReadAll(os.Stdin)
 	if err != nil {
+		Debug("Failed to read secret from stdin", "error", err)
 		return fmt.Errorf("failed to read secret from stdin: %w", err)
 	}
+	Debug("Read secret value from stdin", "value_length", len(value))
 
 	// Remove trailing newline if present
 	if len(value) > 0 && value[len(value)-1] == '\n' {
 		value = value[:len(value)-1]
+		Debug("Removed trailing newline", "new_length", len(value))
 	}
 
-	return vault.AddSecret(secretName, value, force)
+	Debug("Calling vault.AddSecret", "secret_name", secretName, "value_length", len(value), "force", force)
+	err = vault.AddSecret(secretName, value, force)
+	if err != nil {
+		Debug("vault.AddSecret failed", "error", err)
+		return err
+	}
+	Debug("vault.AddSecret completed successfully")
+
+	return nil
 }
 
 // GetSecret retrieves a secret from the vault
@@ -777,27 +809,9 @@ func (cli *CLIInstance) GetSecret(secretName string) error {
 		return err
 	}
 
-	// Get the secret object
-	secret, err := vault.GetSecretObject(secretName)
-	if err != nil {
-		return err
-	}
-
-	// Get the value using the current unlock key (or mnemonic if available)
-	var value []byte
-	if os.Getenv(EnvMnemonic) != "" {
-		// If mnemonic is available, GetValue can handle it without an unlock key
-		value, err = secret.GetValue(nil)
-	} else {
-		// Get the current unlock key
-		unlockKey, unlockErr := vault.GetCurrentUnlockKey()
-		if unlockErr != nil {
-			return fmt.Errorf("failed to get current unlock key: %w", unlockErr)
-		}
-
-		value, err = secret.GetValue(unlockKey)
-	}
-
+	// Get the secret value using the vault's GetSecret method
+	// This handles the per-secret key architecture internally
+	value, err := vault.GetSecret(secretName)
 	if err != nil {
 		return err
 	}
@@ -1037,20 +1051,33 @@ func (cli *CLIInstance) KeysList(jsonOutput bool) error {
 func (cli *CLIInstance) KeysAdd(keyType string, cmd *cobra.Command) error {
 	switch keyType {
 	case "passphrase":
+		// Get current vault
+		vault, err := GetCurrentVault(cli.fs, cli.stateDir)
+		if err != nil {
+			return fmt.Errorf("failed to get current vault: %w", err)
+		}
+
+		// Try to unlock the vault if not already unlocked
+		if vault.Locked() {
+			_, err := vault.UnlockVault()
+			if err != nil {
+				return fmt.Errorf("failed to unlock vault: %w", err)
+			}
+		}
+
 		// Check if passphrase is set in environment variable
 		var passphraseStr string
 		if envPassphrase := os.Getenv(EnvUnlockPassphrase); envPassphrase != "" {
 			passphraseStr = envPassphrase
 		} else {
 			// Use secure passphrase input with confirmation
-			var err error
 			passphraseStr, err = readSecurePassphrase("Enter passphrase for unlock key: ")
 			if err != nil {
 				return fmt.Errorf("failed to read passphrase: %w", err)
 			}
 		}
 
-		passphraseKey, err := CreatePassphraseKey(cli.fs, cli.stateDir, passphraseStr)
+		passphraseKey, err := vault.CreatePassphraseKey(passphraseStr)
 		if err != nil {
 			return err
 		}
@@ -1374,6 +1401,11 @@ func isValidAgeSecretKey(key string) bool {
 // readSecurePassphrase reads a passphrase securely from the terminal without echoing
 // and prompts for confirmation. Falls back to regular input when not on a terminal.
 func readSecurePassphrase(prompt string) (string, error) {
+	// Check if stderr is a terminal - if not, we can't prompt interactively
+	if !term.IsTerminal(int(syscall.Stderr)) {
+		return "", fmt.Errorf("cannot prompt for passphrase: stderr is not a terminal (running in non-interactive mode)")
+	}
+
 	// Check if stdin is a terminal
 	if !term.IsTerminal(int(syscall.Stdin)) {
 		// Not a terminal (piped input, testing, etc.) - use shared line reader
@@ -1390,22 +1422,22 @@ func readSecurePassphrase(prompt string) (string, error) {
 	}
 
 	// Terminal input - use secure password reading with confirmation
-	fmt.Print(prompt)
+	fmt.Fprint(os.Stderr, prompt) // Write prompt to stderr, not stdout
 
 	// Read first passphrase
 	passphrase1, err := term.ReadPassword(int(syscall.Stdin))
 	if err != nil {
 		return "", fmt.Errorf("failed to read passphrase: %w", err)
 	}
-	fmt.Println() // Print newline since ReadPassword doesn't echo
+	fmt.Fprintln(os.Stderr) // Print newline to stderr since ReadPassword doesn't echo
 
 	// Read confirmation passphrase
-	fmt.Print("Confirm passphrase: ")
+	fmt.Fprint(os.Stderr, "Confirm passphrase: ") // Write prompt to stderr, not stdout
 	passphrase2, err := term.ReadPassword(int(syscall.Stdin))
 	if err != nil {
 		return "", fmt.Errorf("failed to read passphrase confirmation: %w", err)
 	}
-	fmt.Println() // Print newline since ReadPassword doesn't echo
+	fmt.Fprintln(os.Stderr) // Print newline to stderr since ReadPassword doesn't echo
 
 	// Compare passphrases
 	if string(passphrase1) != string(passphrase2) {
@@ -1444,6 +1476,10 @@ func (cli *CLIInstance) importMnemonic(vaultName, mnemonic string) error {
 		return fmt.Errorf("failed to write long-term public key: %w", err)
 	}
 
+	// Get the vault instance and unlock it
+	vault := NewVault(cli.fs, vaultName, cli.stateDir)
+	vault.Unlock(ltIdentity)
+
 	// Get or create passphrase for unlock key
 	var passphraseStr string
 	if envPassphrase := os.Getenv(EnvUnlockPassphrase); envPassphrase != "" {
@@ -1456,38 +1492,12 @@ func (cli *CLIInstance) importMnemonic(vaultName, mnemonic string) error {
 		}
 	}
 
-	// Create passphrase-protected unlock key
-	passphraseKey, err := CreatePassphraseKey(cli.fs, cli.stateDir, passphraseStr)
+	// Create passphrase-protected unlock key (vault is now unlocked)
+	passphraseKey, err := vault.CreatePassphraseKey(passphraseStr)
 	if err != nil {
 		return fmt.Errorf("failed to create unlock key: %w", err)
 	}
 
-	// Encrypt long-term private key to the unlock key
-	unlockKeyDir := passphraseKey.GetDirectory()
-
-	// Read unlock key public key
-	unlockPubKeyData, err := afero.ReadFile(cli.fs, filepath.Join(unlockKeyDir, "pub.age"))
-	if err != nil {
-		return fmt.Errorf("failed to read unlock key public key: %w", err)
-	}
-
-	unlockRecipient, err := age.ParseX25519Recipient(string(unlockPubKeyData))
-	if err != nil {
-		return fmt.Errorf("failed to parse unlock key public key: %w", err)
-	}
-
-	// Encrypt long-term private key to unlock key
-	ltPrivKeyData := []byte(ltIdentity.String())
-	encryptedLtPrivKey, err := encryptToRecipient(ltPrivKeyData, unlockRecipient)
-	if err != nil {
-		return fmt.Errorf("failed to encrypt long-term private key: %w", err)
-	}
-
-	// Write encrypted long-term private key
-	if err := afero.WriteFile(cli.fs, filepath.Join(unlockKeyDir, "longterm.age"), encryptedLtPrivKey, 0600); err != nil {
-		return fmt.Errorf("failed to write encrypted long-term private key: %w", err)
-	}
-
 	fmt.Printf("Successfully imported mnemonic into vault '%s'\n", vaultName)
 	fmt.Printf("Long-term public key: %s\n", ltPubKey)
 	fmt.Printf("Unlock key ID: %s\n", passphraseKey.GetMetadata().ID)
diff --git a/internal/secret/crypto.go b/internal/secret/crypto.go
index e1909ea..fa47381 100644
--- a/internal/secret/crypto.go
+++ b/internal/secret/crypto.go
@@ -4,6 +4,7 @@ import (
 	"bytes"
 	"fmt"
 	"io"
+	"os"
 	"syscall"
 
 	"filippo.io/age"
@@ -12,21 +13,34 @@ import (
 
 // encryptToRecipient encrypts data to a recipient using age
 func encryptToRecipient(data []byte, recipient age.Recipient) ([]byte, error) {
+	Debug("encryptToRecipient starting", "data_length", len(data))
+
 	var buf bytes.Buffer
+	Debug("Creating age encryptor")
 	w, err := age.Encrypt(&buf, recipient)
 	if err != nil {
+		Debug("Failed to create encryptor", "error", err)
 		return nil, fmt.Errorf("failed to create encryptor: %w", err)
 	}
+	Debug("Created age encryptor successfully")
 
+	Debug("Writing data to encryptor")
 	if _, err := w.Write(data); err != nil {
+		Debug("Failed to write data to encryptor", "error", err)
 		return nil, fmt.Errorf("failed to write data: %w", err)
 	}
+	Debug("Wrote data to encryptor successfully")
 
+	Debug("Closing encryptor")
 	if err := w.Close(); err != nil {
+		Debug("Failed to close encryptor", "error", err)
 		return nil, fmt.Errorf("failed to close encryptor: %w", err)
 	}
+	Debug("Closed encryptor successfully")
 
-	return buf.Bytes(), nil
+	result := buf.Bytes()
+	Debug("encryptToRecipient completed successfully", "result_length", len(result))
+	return result, nil
 }
 
 // decryptWithIdentity decrypts data with an identity using age
@@ -67,25 +81,24 @@ func decryptWithPassphrase(encryptedData []byte, passphrase string) ([]byte, err
 // readPassphrase reads a passphrase securely from the terminal without echoing
 // This version is for unlocking and doesn't require confirmation
 func readPassphrase(prompt string) (string, error) {
+	// Check if stderr is a terminal - if not, we can't prompt interactively
+	if !term.IsTerminal(int(syscall.Stderr)) {
+		return "", fmt.Errorf("cannot prompt for passphrase: stderr is not a terminal (running in non-interactive mode)")
+	}
+
 	// Check if stdin is a terminal
 	if !term.IsTerminal(int(syscall.Stdin)) {
-		// Not a terminal - fall back to regular input
-		fmt.Print(prompt)
-		var passphrase string
-		_, err := fmt.Scanln(&passphrase)
-		if err != nil {
-			return "", fmt.Errorf("failed to read passphrase: %w", err)
-		}
-		return passphrase, nil
+		// Not a terminal - use shared line reader to avoid buffering conflicts
+		return readLineFromStdin(prompt)
 	}
 
 	// Terminal input - use secure password reading
-	fmt.Print(prompt)
+	fmt.Fprint(os.Stderr, prompt) // Write prompt to stderr, not stdout
 	passphrase, err := term.ReadPassword(int(syscall.Stdin))
 	if err != nil {
 		return "", fmt.Errorf("failed to read passphrase: %w", err)
 	}
-	fmt.Println() // Print newline since ReadPassword doesn't echo
+	fmt.Fprintln(os.Stderr) // Print newline to stderr since ReadPassword doesn't echo
 
 	if len(passphrase) == 0 {
 		return "", fmt.Errorf("passphrase cannot be empty")