Lock the state directory and write vault files atomically (closes #34)

Each command that changes the state directory holds one lock: flock(2)
on `lock` in the state directory, dropped by the kernel if the process
dies, or a process-wide mutex on the in-memory test filesystem. It
covers the state directory, not each vault, because `currentvault`,
`vault create` and cross-vault moves span vaults, and a lock file in a
vault would be deleted by `vault remove` under a waiting command.

Files go through `secret.WriteFileAtomic`; versions, new secrets and
cross-vault copies are built in a temporary directory and renamed into
place; removals rename out of the way first. An unlocker added under
an existing unlocker's directory name is still rewritten file by file:
#71.

Model: opus-5-5

internal/cli/secrets.go

@@ -377,6 +377,15 @@ func (cli *Instance) AddSecret(secretName string, force bool) error {
 	valueBuffer := combineBuffers(buffers, totalSize)
 	defer valueBuffer.Destroy()
 
+	// Locked only now that stdin has been read: in `secret encrypt key |
+	// secret add name`, holding the lock while reading would leave each
+	// command waiting for the other.
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Add the secret to the vault
 	secret.Debug("Calling vault.AddSecret", "secret_name", secretName,
 		"value_length", valueBuffer.Size(), "force", force)
@@ -635,6 +644,14 @@ func (cli *Instance) ImportSecret(
 	valueBuffer := combineBuffers(buffers, totalSize)
 	defer valueBuffer.Destroy()
 
+	// Locked only now that the file has been read, as in AddSecret: the
+	// file may be a pipe written by another secret command.
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Store the secret in the vault
 	err = vlt.AddSecret(secretName, valueBuffer, force)
 	if err != nil {
@@ -649,6 +666,12 @@ func (cli *Instance) ImportSecret(
 
 // RemoveSecret removes a secret from the vault
 func (cli *Instance) RemoveSecret(cmd *cobra.Command, secretName string, _ bool) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Get current vault
 	currentVlt, err := vault.GetCurrentVault(cli.fs, cli.stateDir)
 	if err != nil {
@@ -683,7 +706,7 @@ func (cli *Instance) RemoveSecret(cmd *cobra.Command, secretName string, _ bool)
 	}
 
 	// Remove the secret directory
-	err = cli.fs.RemoveAll(secretDir)
+	err = secret.RemoveDirAtomic(cli.fs, secretDir)
 	if err != nil {
 		return fmt.Errorf("failed to remove secret: %w", err)
 	}
@@ -698,6 +721,12 @@ func (cli *Instance) RemoveSecret(cmd *cobra.Command, secretName string, _ bool)
 func (cli *Instance) MoveSecret(
 	cmd *cobra.Command, source, dest string, force bool,
 ) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Parse source and destination
 	srcVaultName, srcSecretName, srcQualified := ParseVaultSecretRef(source)
 	destVaultName, destSecretName, destQualified := ParseVaultSecretRef(dest)
@@ -792,7 +821,7 @@ func (cli *Instance) moveSecretWithinVault(
 			return fmt.Errorf("secret '%s' %w", dest, errSecretExistsNoForce)
 		}
 
-		err = cli.fs.RemoveAll(destDir)
+		err = secret.RemoveDirAtomic(cli.fs, destDir)
 		if err != nil {
 			return fmt.Errorf("failed to remove existing destination: %w", err)
 		}
@@ -872,7 +901,7 @@ func (cli *Instance) moveSecretCrossVault(
 	}
 
 	// Delete source secret
-	err = cli.fs.RemoveAll(srcSecretDir)
+	err = secret.RemoveDirAtomic(cli.fs, srcSecretDir)
 	if err != nil {
 		// Copy succeeded but delete failed - warn but don't fail
 		cmd.Printf("Warning: copied secret but failed to remove source: %v\n", err)