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

TODO.md

@@ -25,13 +25,21 @@ Bring the repo into policy compliance in one commit:
 
 # Completed Steps
 
-- 2026-10-03: Key material is wiped on every exit: `Entry()` returns
-  the exit code after its deferred `memguard.Purge()` has run, and only
-  `main` calls `os.Exit`. SIGINT and SIGTERM go through memguard's
-  handler, which wipes every buffer before exiting; when the process is
-  in the terminal's foreground process group it first restores the
-  terminal settings from startup, so an interrupted passphrase prompt no
-  longer leaves echo off.
+- 2026-10-03: Commands that change the state directory hold one lock
+  (`flock` on `lock` in the state directory; a mutex on the in-memory
+  test filesystem), so concurrent commands no longer lose versions or
+  race on the current pointers. Every file is written through
+  `secret.WriteFileAtomic` (temporary file, sync, rename); new
+  versions, new secrets and cross-vault copies are built in a
+  temporary directory and renamed into place, and removals rename out
+  of the way first, so an interrupted command leaves nothing
+  half-written, with one exception: an unlocker added under the
+  directory name of an existing one is rewritten in place, file by
+  file, and a crash part-way leaves it unable to open the vault. That
+  happens to a passphrase unlocker added to a vault that has one, and
+  to a PGP, keychain or Secure Enclave unlocker added on the same host
+  and day as another of its type
+  (https://git.eeqj.de/sneak/secret/issues/71).
 - 2026-10-02: A plain `docker build .` builds again: the size tests
   skip a case that needs more locked memory than the process can
   lock, and run every case under `script/cibuild`. The image stamps the
@@ -101,8 +109,6 @@ Bring the repo into policy compliance in one commit:
       pgpunlocker.go:256, version.go:155); age secret key held in a
       plain string in cli/crypto.go:86,91,113; private keys exposed via
       buffer.Bytes() to GPGEncryptFunc and EncryptWithPassphrase.
-    - Race conditions: no file locking in vault/secrets.go:142-176;
-      non-atomic writes can leave the vault inconsistent.
     - Input validation: dots in secret names risk path traversal
       (vault/secrets.go:75-99); no maximum secret size (DoS).
     - Timing attacks: bytes.Equal passphrase compare (cli/init.go:

cmd/secret/main.go

@@ -1,12 +1,8 @@
 // Package main is the entry point for the secret CLI application.
 package main
 
-import (
-	"os"
-
-	"git.eeqj.de/sneak/secret/internal/cli"
-)
+import "git.eeqj.de/sneak/secret/internal/cli"
 
 func main() {
-	os.Exit(cli.Entry())
+	cli.Entry()
 }

internal/cli/crypto.go

@@ -72,10 +72,18 @@ func newDecryptCmd() *cobra.Command {
 
 // resolveEncryptionKey returns a secure buffer holding the age secret key
 // for the named secret, generating and storing a new key if the secret
-// does not exist. The caller must destroy the returned buffer.
+// does not exist. The caller must destroy the returned buffer. It holds the
+// state directory lock itself, so that Encrypt streams its input and output
+// unlocked and cannot block a secret command at the other end of a pipe.
 func (cli *Instance) resolveEncryptionKey(
 	vlt *vault.Vault, secretName string,
 ) (*memguard.LockedBuffer, error) {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return nil, err
+	}
+	defer release()
+
 	// Check if secret exists
 	secretObj := secret.NewSecret(vlt, secretName)
 

internal/cli/entry_test.go

@@ -1,108 +0,0 @@
-package cli_test
-
-import (
-	"bufio"
-	"context"
-	"os"
-	"os/exec"
-	"path/filepath"
-	"strings"
-	"testing"
-	"time"
-
-	"git.eeqj.de/sneak/secret/internal/cli"
-	"git.eeqj.de/sneak/secret/internal/secret"
-	"github.com/awnumar/memguard"
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-// Entry must return its exit code rather than exit, so that its deferred
-// memguard purge runs on the success and the error path alike.
-//
-//nolint:paralleltest // sets os.Args, and Entry wipes every buffer in the process
-func TestEntryWipesBuffersAndReturnsExitCode(t *testing.T) {
-	savedArgs := os.Args
-
-	t.Cleanup(func() { os.Args = savedArgs })
-
-	tests := []struct {
-		args     []string
-		exitCode int
-	}{
-		{args: []string{"secret", "--help"}, exitCode: 0},
-		{args: []string{"secret", "no-such-command"}, exitCode: 1},
-	}
-
-	for _, tt := range tests {
-		buf := memguard.NewBufferFromBytes([]byte("key material"))
-		os.Args = tt.args
-
-		assert.Equal(t, tt.exitCode, cli.Entry(), "exit code for %v", tt.args)
-		assert.False(t, buf.IsAlive(), "Entry left a buffer unwiped for %v", tt.args)
-	}
-}
-
-// Ctrl-C while `secret add` waits for the value on stdin must end the
-// process through memguard's signal handler, which wipes every buffer and
-// exits with status 1, not through Go's default handling, which kills the
-// process with the buffers intact.
-func TestInterruptExitsThroughMemguard(t *testing.T) {
-	t.Parallel()
-
-	const waitingForValue = "Reading secret value from stdin"
-
-	ctx, cancel := context.WithTimeout(t.Context(), time.Minute)
-	defer cancel()
-
-	wd, err := filepath.Abs("../..")
-	require.NoError(t, err)
-
-	secretPath := filepath.Join(wd, "secret")
-	env := []string{
-		secret.EnvStateDir + "=" + t.TempDir(),
-		secret.EnvMnemonic + "=" + testMnemonic,
-		secret.EnvUnlockPassphrase + "=test-passphrase",
-		"PATH=/usr/bin:/bin",
-		// The debug log on stderr shows when add starts waiting for the value.
-		"GODEBUG=berlin.sneak.pkg.secret",
-	}
-
-	//nolint:gosec // G204: test executes the freshly built secret binary
-	initCmd := exec.CommandContext(ctx, secretPath, "init")
-	initCmd.Env = env
-
-	output, err := initCmd.CombinedOutput()
-	require.NoError(t, err, "init should succeed: %s", output)
-
-	//nolint:gosec // G204: test executes the freshly built secret binary
-	addCmd := exec.CommandContext(ctx, secretPath, "add", "test/secret")
-	addCmd.Env = env
-
-	// Held open and never written, so add keeps waiting for the value.
-	stdin, err := addCmd.StdinPipe()
-	require.NoError(t, err)
-
-	defer func() { _ = stdin.Close() }()
-
-	stderr, err := addCmd.StderrPipe()
-	require.NoError(t, err)
-	require.NoError(t, addCmd.Start())
-
-	waiting := false
-
-	scanner := bufio.NewScanner(stderr)
-	for !waiting && scanner.Scan() {
-		waiting = strings.Contains(scanner.Text(), waitingForValue)
-	}
-
-	require.True(t, waiting, "add never logged %q", waitingForValue)
-	require.NoError(t, addCmd.Process.Signal(os.Interrupt))
-
-	err = addCmd.Wait()
-
-	var exitErr *exec.ExitError
-
-	require.ErrorAs(t, err, &exitErr)
-	assert.Equal(t, 1, exitErr.ExitCode(), "add ended with %v", err)
-}

internal/cli/generate.go

@@ -155,6 +155,12 @@ func (cli *Instance) GenerateSecret(
 		return fmt.Errorf("failed to generate random secret: %w", err)
 	}
 
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Store the secret in the vault
 	vlt, err := vault.GetCurrentVault(cli.fs, cli.stateDir)
 	if err != nil {

internal/cli/init.go

@@ -103,8 +103,21 @@ func (cli *Instance) setupDefaultVault(
 	return vlt, ltIdentity, nil
 }
 
-// Init initializes the secret manager
+// Init initializes the secret manager, holding the state directory lock
+// while initialize runs
 func (cli *Instance) Init(cmd *cobra.Command) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
+	return cli.initialize(cmd)
+}
+
+// initialize creates the state directory, the default vault and its first
+// unlocker
+func (cli *Instance) initialize(cmd *cobra.Command) error {
 	secret.Debug("Starting secret manager initialization")
 
 	// Create state directory

internal/cli/lock_test.go

@@ -0,0 +1,224 @@
+//nolint:testpackage // sets the unexported fields of Instance
+package cli
+
+import (
+	"io"
+	"path/filepath"
+	"strconv"
+	"strings"
+	"sync"
+	"testing"
+	"time"
+
+	"git.eeqj.de/sneak/secret/internal/secret"
+	"git.eeqj.de/sneak/secret/internal/vault"
+	"github.com/spf13/afero"
+	"github.com/spf13/cobra"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// addAtOnce runs one add of the secret name per value, all at once, and
+// returns their errors.
+func addAtOnce(
+	fs afero.Fs, stateDir, name string, force bool, values []string,
+) []error {
+	errs := make(chan error, len(values))
+
+	for _, value := range values {
+		go func() {
+			cli := NewCLIInstanceWithStateDir(fs, stateDir)
+			cli.cmd = &cobra.Command{}
+			cli.cmd.SetIn(strings.NewReader(value))
+
+			errs <- cli.AddSecret(name, force)
+		}()
+	}
+
+	results := make([]error, 0, len(values))
+	for range values {
+		results = append(results, <-errs)
+	}
+
+	return results
+}
+
+// numbered returns count distinct values starting with prefix.
+func numbered(prefix string, count int) []string {
+	values := make([]string, 0, count)
+	for i := range count {
+		values = append(values, prefix+"-"+strconv.Itoa(i))
+	}
+
+	return values
+}
+
+// TestConcurrentAddsKeepEveryVersion runs adds of one secret at once, on
+// the in-memory and on the real filesystem. Without the state directory
+// lock, adds of a new secret all find it absent and replace each other, and
+// forced adds read the same highest version number and overwrite each
+// other's version. With it they behave as if run one after another.
+//
+//nolint:paralleltest // t.Setenv forbids parallel subtests
+func TestConcurrentAddsKeepEveryVersion(t *testing.T) {
+	t.Setenv(secret.EnvMnemonic, testMnemonic)
+
+	const adds = 8
+
+	for _, tc := range []struct {
+		name     string
+		fs       afero.Fs
+		stateDir string
+	}{
+		{"memory", afero.NewMemMapFs(), testStateDir},
+		{"real", afero.NewOsFs(), t.TempDir()},
+	} {
+		t.Run(tc.name, func(t *testing.T) {
+			_, err := vault.CreateVault(tc.fs, tc.stateDir, "default")
+			require.NoError(t, err)
+
+			// One add creates the secret; the others find that it exists
+			created := 0
+
+			for _, err := range addAtOnce(tc.fs, tc.stateDir, "shared", false,
+				numbered("create", adds)) {
+				if err == nil {
+					created++
+				} else {
+					require.ErrorIs(t, err, vault.ErrSecretExists)
+				}
+			}
+
+			require.Equal(t, 1, created, "exactly one add creates the secret")
+
+			// Every forced add stores a version of its own
+			for _, err := range addAtOnce(tc.fs, tc.stateDir, "shared", true,
+				numbered("force", adds)) {
+				require.NoError(t, err)
+			}
+
+			vlt, err := vault.GetCurrentVault(tc.fs, tc.stateDir)
+			require.NoError(t, err)
+
+			vaultDir, err := vlt.GetDirectory()
+			require.NoError(t, err)
+
+			versions, err := secret.ListVersions(tc.fs,
+				filepath.Join(vaultDir, "secrets.d", "shared"))
+			require.NoError(t, err)
+			require.Len(t, versions, adds+1, "one version per successful add")
+
+			values := make(map[string]bool, len(versions))
+
+			for _, version := range versions {
+				value, err := vlt.GetSecretVersion("shared", version)
+				require.NoError(t, err)
+
+				values[string(value)] = true
+			}
+
+			assert.Len(t, values, adds+1, "every add stored its own value")
+		})
+	}
+}
+
+// readNotifier passes reads through to Reader and closes reading at the
+// first one.
+type readNotifier struct {
+	io.Reader
+
+	reading chan struct{}
+	once    sync.Once
+}
+
+func (r *readNotifier) Read(p []byte) (int, error) {
+	r.once.Do(func() { close(r.reading) })
+
+	return r.Reader.Read(p)
+}
+
+// TestEncryptPipedIntoAdd runs `secret encrypt key | secret add name` in
+// one process, starting encrypt once add is reading its input. Had add
+// taken the state directory lock before reading, it would hold the lock
+// while waiting for encrypt's output, and encrypt would wait for the lock
+// to store its key: neither would finish.
+func TestEncryptPipedIntoAdd(t *testing.T) {
+	t.Setenv(secret.EnvMnemonic, testMnemonic)
+
+	fs := afero.NewMemMapFs()
+	_, err := vault.CreateVault(fs, testStateDir, "default")
+	require.NoError(t, err)
+	require.NoError(t, afero.WriteFile(fs, "/plaintext", []byte("piped"), 0o600))
+
+	pipeReader, pipeWriter := io.Pipe()
+	// If the test gives up, this makes add's read fail, so that both
+	// commands return and release the lock the other tests use
+	t.Cleanup(func() { _ = pipeReader.Close() })
+
+	const commands = 2
+
+	input := &readNotifier{Reader: pipeReader, reading: make(chan struct{})}
+	results := make(chan error, commands)
+
+	go func() {
+		add := NewCLIInstanceWithStateDir(fs, testStateDir)
+		add.cmd = &cobra.Command{}
+		add.cmd.SetIn(input)
+
+		results <- add.AddSecret("encrypted", false)
+	}()
+
+	go func() {
+		<-input.reading
+
+		encrypt := NewCLIInstanceWithStateDir(fs, testStateDir)
+		encrypt.cmd = &cobra.Command{}
+		encrypt.cmd.SetOut(pipeWriter)
+
+		err := encrypt.Encrypt("key", "/plaintext", "")
+		// Ends add's input, as the end of the pipe does
+		_ = pipeWriter.CloseWithError(err)
+
+		results <- err
+	}()
+
+	timeout := time.After(10 * time.Second)
+
+	for range commands {
+		select {
+		case err := <-results:
+			require.NoError(t, err)
+		case <-timeout:
+			t.Fatal("secret encrypt piped into secret add never finished")
+		}
+	}
+}
+
+// TestFailedCommandReleasesLock checks that a command failing after it
+// took the state directory lock leaves the lock free for the next command.
+func TestFailedCommandReleasesLock(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewMemMapFs()
+	cli := NewCLIInstanceWithStateDir(fs, testStateDir)
+
+	// Fails once it holds the lock: there is no current vault
+	err := cli.RemoveSecret(&cobra.Command{}, "missing", false)
+	require.Error(t, err)
+
+	taken := make(chan func(), 1)
+
+	go func() {
+		release, err := vault.LockStateDir(fs, testStateDir)
+		if assert.NoError(t, err) {
+			taken <- release
+		}
+	}()
+
+	select {
+	case release := <-taken:
+		release()
+	case <-time.After(10 * time.Second):
+		t.Fatal("the failed command left the state directory locked")
+	}
+}

internal/cli/root.go

@@ -4,38 +4,17 @@ import (
 	"os"
 
 	"git.eeqj.de/sneak/secret/internal/secret"
-	"github.com/awnumar/memguard"
 	"github.com/spf13/cobra"
-	"golang.org/x/sys/unix"
-	"golang.org/x/term"
 )
 
-// Entry runs the secret CLI and returns the process exit code. It wipes
-// every memguard buffer before it returns, so the caller must do nothing
-// but exit with the code.
-func Entry() int {
-	// On SIGINT or SIGTERM memguard runs this function, wipes every buffer
-	// and exits with status 1. The passphrase prompt turns terminal echo
-	// off until the read finishes, so a signal there would leave echo off.
-	// Only a process in the terminal's foreground process group may reset
-	// it: one in the background that tries is stopped instead of exiting.
-	terminalState, terminalErr := term.GetState(unix.Stdin)
+// Entry is the entry point for the secret CLI application
+func Entry() {
+	cmd := newRootCmd()
 
-	memguard.CatchSignal(func(os.Signal) {
-		foreground, err := unix.IoctlGetInt(unix.Stdin, unix.TIOCGPGRP)
-		if terminalErr == nil && err == nil && foreground == unix.Getpgrp() {
-			_ = term.Restore(unix.Stdin, terminalState)
-		}
-	}, os.Interrupt, unix.SIGTERM)
-
-	defer memguard.Purge()
-
-	err := newRootCmd().Execute()
+	err := cmd.Execute()
 	if err != nil {
-		return 1
+		os.Exit(1)
 	}
-
-	return 0
 }
 
 func newRootCmd() *cobra.Command {

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)

internal/cli/unlockers.go

@@ -534,6 +534,12 @@ func (cli *Instance) printUnlockersTable(unlockers []UnlockerInfo) error {
 
 // UnlockersAdd adds a new unlocker
 func (cli *Instance) UnlockersAdd(unlockerType string, cmd *cobra.Command) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	switch unlockerType {
 	case unlockerTypePassphrase:
 		return cli.addPassphraseUnlocker(cmd)
@@ -714,6 +720,12 @@ func (cli *Instance) addPGPUnlocker(cmd *cobra.Command) error {
 func (cli *Instance) UnlockersRemove(
 	unlockerID string, force bool, cmd *cobra.Command,
 ) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Get current vault
 	vlt, err := vault.GetCurrentVault(cli.fs, cli.stateDir)
 	if err != nil {
@@ -763,6 +775,12 @@ func (cli *Instance) UnlockersRemove(
 
 // UnlockerSelect selects an unlocker as current
 func (cli *Instance) UnlockerSelect(unlockerID string) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Get current vault
 	vlt, err := vault.GetCurrentVault(cli.fs, cli.stateDir)
 	if err != nil {

internal/cli/vault.go

@@ -267,6 +267,12 @@ func resolvePassphrase() (*memguard.LockedBuffer, error) {
 func (cli *Instance) CreateVault(cmd *cobra.Command, name string) error {
 	secret.Debug("Creating new vault", "name", name, "state_dir", cli.stateDir)
 
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Get or prompt for mnemonic
 	var mnemonicStr string
 
@@ -354,7 +360,13 @@ func (cli *Instance) CreateVault(cmd *cobra.Command, name string) error {
 
 // SelectVault selects a vault as the current one
 func (cli *Instance) SelectVault(cmd *cobra.Command, name string) error {
-	err := vault.SelectVault(cli.fs, cli.stateDir, name)
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
+	err = vault.SelectVault(cli.fs, cli.stateDir, name)
 	if err != nil {
 		return err
 	}
@@ -442,8 +454,21 @@ func updateVaultImportMetadata(
 	return nil
 }
 
-// VaultImport imports a mnemonic into a specific vault
+// VaultImport imports a mnemonic into a specific vault, holding the state
+// directory lock while importMnemonic runs
 func (cli *Instance) VaultImport(cmd *cobra.Command, vaultName string) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
+	return cli.importMnemonic(cmd, vaultName)
+}
+
+// importMnemonic gives the vault a long-term key derived from the mnemonic
+// and a passphrase unlocker
+func (cli *Instance) importMnemonic(cmd *cobra.Command, vaultName string) error {
 	secret.Debug("Importing mnemonic into vault",
 		"vault_name", vaultName, "state_dir", cli.stateDir)
 
@@ -478,7 +503,7 @@ func (cli *Instance) VaultImport(cmd *cobra.Command, vaultName string) error {
 	secret.Debug("Storing long-term public key",
 		"pubkey", ltPublicKey, "vault_dir", vaultDir)
 
-	err = afero.WriteFile(cli.fs, pubKeyPath, []byte(ltPublicKey), secret.FilePerms)
+	err = secret.WriteFileAtomic(cli.fs, pubKeyPath, []byte(ltPublicKey))
 	if err != nil {
 		return fmt.Errorf("failed to store long-term public key: %w", err)
 	}
@@ -577,6 +602,12 @@ func (cli *Instance) switchAwayFromVault(
 
 // RemoveVault removes a vault with safety checks
 func (cli *Instance) RemoveVault(cmd *cobra.Command, name string, force bool) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Get list of all vaults
 	vaults, err := vault.ListVaults(cli.fs, cli.stateDir)
 	if err != nil {
@@ -626,7 +657,7 @@ func (cli *Instance) RemoveVault(cmd *cobra.Command, name string, force bool) er
 	}
 
 	// Remove the vault directory
-	err = cli.fs.RemoveAll(vaultDir)
+	err = secret.RemoveDirAtomic(cli.fs, vaultDir)
 	if err != nil {
 		return fmt.Errorf("failed to remove vault directory: %w", err)
 	}

internal/cli/version.go

@@ -239,6 +239,12 @@ func formatVersionTime(t *time.Time) string {
 func (cli *Instance) PromoteVersion(
 	cmd *cobra.Command, secretName string, version string,
 ) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Get current vault
 	vlt, err := vault.GetCurrentVault(cli.fs, cli.stateDir)
 	if err != nil {
@@ -282,6 +288,12 @@ func (cli *Instance) PromoteVersion(
 func (cli *Instance) RemoveVersion(
 	cmd *cobra.Command, secretName string, version string,
 ) error {
+	release, err := vault.LockStateDir(cli.fs, cli.stateDir)
+	if err != nil {
+		return err
+	}
+	defer release()
+
 	// Get current vault
 	vlt, err := vault.GetCurrentVault(cli.fs, cli.stateDir)
 	if err != nil {
@@ -333,7 +345,7 @@ func (cli *Instance) RemoveVersion(
 	}
 
 	// Remove the version directory
-	err = cli.fs.RemoveAll(versionDir)
+	err = secret.RemoveDirAtomic(cli.fs, versionDir)
 	if err != nil {
 		return fmt.Errorf("failed to remove version: %w", err)
 	}

internal/secret/atomic.go

@@ -0,0 +1,86 @@
+package secret
+
+import (
+	"fmt"
+	"path/filepath"
+
+	"github.com/spf13/afero"
+)
+
+// WriteFileAtomic replaces the file at path with data so that a reader, or
+// a crash at any moment, finds either the old content or the new, never a
+// partial file. The data goes into a temporary file that afero.TempFile
+// creates with mode 0600 in the same directory (a rename is only atomic
+// within one filesystem), is synced to disk, and is renamed over path. The
+// temporary file is removed if any step fails.
+func WriteFileAtomic(fs afero.Fs, path string, data []byte) error {
+	tmp, err := afero.TempFile(fs, filepath.Dir(path),
+		"."+filepath.Base(path)+".tmp-*")
+	if err != nil {
+		return fmt.Errorf("failed to create temporary file for %s: %w", path, err)
+	}
+
+	_, err = tmp.Write(data)
+	if err == nil {
+		err = tmp.Sync()
+	}
+
+	closeErr := tmp.Close()
+	if err == nil {
+		err = closeErr
+	}
+
+	if err == nil {
+		err = fs.Rename(tmp.Name(), path)
+	}
+
+	if err != nil {
+		_ = fs.Remove(tmp.Name())
+
+		return fmt.Errorf("failed to write %s: %w", path, err)
+	}
+
+	return nil
+}
+
+// TempDirFor creates an empty temporary directory in which to build the
+// directory target before renaming it into place, or into which to move
+// target before deleting it. It is made in target's grandparent: on the
+// same filesystem, so the rename is atomic, and outside target's parent,
+// the directory that is listed to find vaults, secrets, versions and
+// unlockers, so one left behind by a crash is never taken for one of them.
+// Its name leaves out target's, which may already be as long as a file name
+// can be.
+func TempDirFor(fs afero.Fs, target string) (string, error) {
+	dir, err := afero.TempDir(fs, filepath.Dir(filepath.Dir(target)), ".tmp-")
+	if err != nil {
+		return "", fmt.Errorf(
+			"failed to create temporary directory for %s: %w", target, err)
+	}
+
+	return dir, nil
+}
+
+// RemoveDirAtomic deletes the directory dir so that it disappears in one
+// rename: dir is moved into a new directory from TempDirFor, which is then
+// deleted. A crash part-way leaves only that temporary directory behind.
+func RemoveDirAtomic(fs afero.Fs, dir string) error {
+	tmp, err := TempDirFor(fs, dir)
+	if err != nil {
+		return err
+	}
+
+	err = fs.Rename(dir, filepath.Join(tmp, filepath.Base(dir)))
+	if err != nil {
+		_ = fs.Remove(tmp)
+
+		return fmt.Errorf("failed to remove %s: %w", dir, err)
+	}
+
+	err = fs.RemoveAll(tmp)
+	if err != nil {
+		return fmt.Errorf("failed to remove %s: %w", dir, err)
+	}
+
+	return nil
+}

internal/secret/atomic_test.go

@@ -0,0 +1,506 @@
+package secret_test
+
+import (
+	"errors"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"filippo.io/age"
+	"git.eeqj.de/sneak/secret/internal/secret"
+	"git.eeqj.de/sneak/secret/internal/vault"
+	"github.com/awnumar/memguard"
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+var errInjected = errors.New("injected failure")
+
+// The kinds of change hookFs passes to before.
+const (
+	opCreate = "create"
+	opOpen   = "open"
+	opMkdir  = "mkdir"
+	opRemove = "remove"
+	opRename = "rename"
+)
+
+// currentFile is the file in a secret's directory that names its current
+// version.
+const currentFile = "current"
+
+// hookFs passes every call through to Fs, but first calls before for each
+// call that changes the filesystem, with the path it changes (the new path,
+// for Rename). A test uses before to inspect the tree at every point where
+// a crash could stop the code under test, or returns an error from it to
+// make that call fail.
+type hookFs struct {
+	afero.Fs
+
+	before func(op, path string) error
+}
+
+//nolint:ireturn // implements afero.Fs
+func (h hookFs) Create(name string) (afero.File, error) {
+	err := h.before(opCreate, name)
+	if err != nil {
+		return nil, err
+	}
+
+	return h.Fs.Create(name)
+}
+
+//nolint:ireturn // implements afero.Fs
+func (h hookFs) OpenFile(
+	name string, flag int, perm os.FileMode,
+) (afero.File, error) {
+	err := h.before(opOpen, name)
+	if err != nil {
+		return nil, err
+	}
+
+	return h.Fs.OpenFile(name, flag, perm)
+}
+
+func (h hookFs) Mkdir(name string, perm os.FileMode) error {
+	err := h.before(opMkdir, name)
+	if err != nil {
+		return err
+	}
+
+	return h.Fs.Mkdir(name, perm)
+}
+
+func (h hookFs) MkdirAll(path string, perm os.FileMode) error {
+	err := h.before(opMkdir, path)
+	if err != nil {
+		return err
+	}
+
+	return h.Fs.MkdirAll(path, perm)
+}
+
+func (h hookFs) Remove(name string) error {
+	err := h.before(opRemove, name)
+	if err != nil {
+		return err
+	}
+
+	return h.Fs.Remove(name)
+}
+
+func (h hookFs) RemoveAll(path string) error {
+	err := h.before(opRemove, path)
+	if err != nil {
+		return err
+	}
+
+	return h.Fs.RemoveAll(path)
+}
+
+func (h hookFs) Rename(oldname, newname string) error {
+	err := h.before(opRename, newname)
+	if err != nil {
+		return err
+	}
+
+	return h.Fs.Rename(oldname, newname)
+}
+
+// testFilesystem is a filesystem to run a test on, with a directory in it
+// to work in.
+type testFilesystem struct {
+	name string
+	open func(t *testing.T) (afero.Fs, string)
+}
+
+// testFilesystems are the in-memory filesystem that most tests use and the
+// real one: every rename-based guarantee is checked on both.
+//
+//nolint:gochecknoglobals // read-only table shared by the tests below
+var testFilesystems = []testFilesystem{
+	{"memory", func(*testing.T) (afero.Fs, string) {
+		return afero.NewMemMapFs(), "/test"
+	}},
+	{"real", func(t *testing.T) (afero.Fs, string) {
+		t.Helper()
+
+		return afero.NewOsFs(), t.TempDir()
+	}},
+}
+
+// dirNames lists the names in dir.
+func dirNames(t *testing.T, fs afero.Fs, dir string) []string {
+	t.Helper()
+
+	entries, err := afero.ReadDir(fs, dir)
+	require.NoError(t, err)
+
+	names := make([]string, 0, len(entries))
+	for _, entry := range entries {
+		names = append(names, entry.Name())
+	}
+
+	return names
+}
+
+// writeLongTermKey gives the test vault under stateDir a new long-term key
+// and returns it.
+func writeLongTermKey(
+	t *testing.T, fs afero.Fs, stateDir string,
+) *age.X25519Identity {
+	t.Helper()
+
+	vault := &MockVersionVault{Name: testVaultName, fs: fs, stateDir: stateDir}
+
+	vaultDir, err := vault.GetDirectory()
+	require.NoError(t, err)
+	require.NoError(t, fs.MkdirAll(vaultDir, 0o700))
+
+	ltIdentity, err := age.GenerateX25519Identity()
+	require.NoError(t, err)
+	require.NoError(t, afero.WriteFile(fs, filepath.Join(vaultDir, "pub.age"),
+		[]byte(ltIdentity.Recipient().String()), 0o600))
+
+	return ltIdentity
+}
+
+// newVaultWithSecret creates the vault name under stateDir from the test
+// mnemonic, with a secret "shared" in it that holds value.
+func newVaultWithSecret(
+	t *testing.T, fs afero.Fs, stateDir, name, value string,
+) *vault.Vault {
+	t.Helper()
+
+	vlt, err := vault.CreateVault(fs, stateDir, name)
+	require.NoError(t, err)
+
+	buffer := memguard.NewBufferFromBytes([]byte(value))
+	defer buffer.Destroy()
+
+	require.NoError(t, vlt.AddSecret("shared", buffer, false))
+
+	return vlt
+}
+
+func TestWriteFileAtomicReplacesFile(t *testing.T) {
+	t.Parallel()
+
+	for _, tfs := range testFilesystems {
+		t.Run(tfs.name, func(t *testing.T) {
+			t.Parallel()
+
+			fs, dir := tfs.open(t)
+			path := filepath.Join(dir, currentFile)
+
+			require.NoError(t, secret.WriteFileAtomic(fs, path, []byte("old")))
+			require.NoError(t, secret.WriteFileAtomic(fs, path, []byte("new")))
+
+			data, err := afero.ReadFile(fs, path)
+			require.NoError(t, err)
+			assert.Equal(t, "new", string(data))
+
+			info, err := fs.Stat(path)
+			require.NoError(t, err)
+			assert.Equal(t, secret.FilePerms, info.Mode().Perm())
+
+			// No temporary file is left next to it
+			assert.Equal(t, []string{currentFile}, dirNames(t, fs, dir))
+		})
+	}
+}
+
+func TestWriteFileAtomicFailureKeepsOldFile(t *testing.T) {
+	t.Parallel()
+
+	for _, tfs := range testFilesystems {
+		t.Run(tfs.name, func(t *testing.T) {
+			t.Parallel()
+
+			base, dir := tfs.open(t)
+			path := filepath.Join(dir, currentFile)
+			require.NoError(t, secret.WriteFileAtomic(base, path, []byte("old")))
+
+			fs := hookFs{Fs: base, before: func(op, _ string) error {
+				if op == opRename {
+					return errInjected
+				}
+
+				return nil
+			}}
+
+			err := secret.WriteFileAtomic(fs, path, []byte("new"))
+			require.ErrorIs(t, err, errInjected)
+
+			data, err := afero.ReadFile(base, path)
+			require.NoError(t, err)
+			assert.Equal(t, "old", string(data))
+
+			// The temporary file is removed again
+			assert.Equal(t, []string{currentFile}, dirNames(t, base, dir))
+		})
+	}
+}
+
+// TestRemoveDirAtomic checks that RemoveDirAtomic deletes nothing where the
+// directory stands, which a crash could stop half-way, and that it leaves
+// nothing behind.
+func TestRemoveDirAtomic(t *testing.T) {
+	t.Parallel()
+
+	for _, tfs := range testFilesystems {
+		t.Run(tfs.name, func(t *testing.T) {
+			t.Parallel()
+
+			base, dir := tfs.open(t)
+			listed := filepath.Join(dir, "secrets.d")
+			target := filepath.Join(listed, "doomed")
+
+			require.NoError(t, base.MkdirAll(filepath.Join(target, "versions"), 0o700))
+			require.NoError(t, secret.WriteFileAtomic(base,
+				filepath.Join(target, currentFile), []byte("20231216.001")))
+
+			fs := hookFs{Fs: base, before: func(op, path string) error {
+				if op == opRemove && strings.HasPrefix(path, target) {
+					t.Errorf("deleted %s where it stands", path)
+				}
+
+				return nil
+			}}
+
+			require.NoError(t, secret.RemoveDirAtomic(fs, target))
+
+			// Gone, and no temporary directory is left in the directory
+			// that is listed or in the one above it
+			assert.Empty(t, dirNames(t, base, listed))
+			assert.Equal(t, []string{"secrets.d"}, dirNames(t, base, dir))
+		})
+	}
+}
+
+// TestLongestNames adds a secret to a vault and removes the vault, both
+// named with 255 bytes, the most a file name may have, on the real
+// filesystem: the temporary directories they use must fit that limit too.
+func TestLongestNames(t *testing.T) {
+	t.Setenv(secret.EnvMnemonic, testMnemonic)
+
+	const longestName = 255
+
+	fs := afero.NewOsFs()
+	name := strings.Repeat("a", longestName)
+
+	vlt, err := vault.CreateVault(fs, t.TempDir(), name)
+	require.NoError(t, err)
+
+	value := memguard.NewBufferFromBytes([]byte("long"))
+	defer value.Destroy()
+
+	require.NoError(t, vlt.AddSecret(name, value, false))
+
+	got, err := vlt.GetSecret(name)
+	require.NoError(t, err)
+	assert.Equal(t, "long", string(got))
+
+	vaultDir, err := vlt.GetDirectory()
+	require.NoError(t, err)
+	require.NoError(t, secret.RemoveDirAtomic(fs, vaultDir))
+	assert.NoDirExists(t, vaultDir)
+}
+
+// TestForcedCopyKeepsDestinationUntilReplaced copies a secret over one in
+// another vault, as a forced move between vaults does, and makes the last
+// step that completes the copy fail. The secret it was to replace must
+// still be there unchanged: it may go only once its replacement is whole.
+//
+//nolint:paralleltest // t.Setenv forbids t.Parallel
+func TestForcedCopyKeepsDestinationUntilReplaced(t *testing.T) {
+	t.Setenv(secret.EnvMnemonic, testMnemonic)
+
+	for _, tfs := range testFilesystems {
+		t.Run(tfs.name, func(t *testing.T) {
+			base, stateDir := tfs.open(t)
+			src := newVaultWithSecret(t, base, stateDir, "source", "new")
+			dest := newVaultWithSecret(t, base, stateDir, "dest", "old")
+
+			// The copy is complete once its current file is written
+			fs := hookFs{Fs: base, before: func(op, path string) error {
+				if op == opRename && filepath.Base(path) == currentFile {
+					return errInjected
+				}
+
+				return nil
+			}}
+
+			err := vault.NewVault(fs, stateDir, "dest").
+				CopySecretAllVersions(src, "shared", "shared", true)
+			require.ErrorIs(t, err, errInjected)
+
+			value, err := dest.GetSecret("shared")
+			require.NoError(t, err)
+			assert.Equal(t, "old", string(value))
+		})
+	}
+}
+
+// TestTempDirsStayOutOfListings adds a version, adds a secret, copies a
+// secret over another and removes one, and checks that none of them makes a
+// directory directly in secrets.d or in a versions directory. Those are
+// listed to find secrets and versions, so a temporary directory made there
+// would be listed while half-built, and one left by a crash would stay.
+//
+//nolint:paralleltest // t.Setenv forbids t.Parallel
+func TestTempDirsStayOutOfListings(t *testing.T) {
+	t.Setenv(secret.EnvMnemonic, testMnemonic)
+
+	for _, tfs := range testFilesystems {
+		t.Run(tfs.name, func(t *testing.T) {
+			base, stateDir := tfs.open(t)
+			newVaultWithSecret(t, base, stateDir, "default", "first")
+
+			fs := hookFs{Fs: base, before: func(op, path string) error {
+				parent := filepath.Base(filepath.Dir(path))
+				if op == opMkdir && (parent == "secrets.d" || parent == "versions") {
+					t.Errorf("made %s where it is listed", path)
+				}
+
+				return nil
+			}}
+			vlt := vault.NewVault(fs, stateDir, "default")
+
+			value := memguard.NewBufferFromBytes([]byte("second"))
+			defer value.Destroy()
+
+			require.NoError(t, vlt.AddSecret("shared", value, true))
+			require.NoError(t, vlt.AddSecret("other", value, false))
+			require.NoError(t, vlt.CopySecretAllVersions(vlt, "shared", "other", true))
+
+			vaultDir, err := vlt.GetDirectory()
+			require.NoError(t, err)
+			require.NoError(t, secret.RemoveDirAtomic(fs,
+				filepath.Join(vaultDir, "secrets.d", "shared")))
+		})
+	}
+}
+
+// TestVersionSaveIsWholeOrAbsent checks, before every change Save makes and
+// once after it returns, that the version directory either does not exist
+// or holds all of its files: a crash at any point leaves no version that
+// cannot be decrypted.
+func TestVersionSaveIsWholeOrAbsent(t *testing.T) {
+	t.Parallel()
+
+	for _, tfs := range testFilesystems {
+		t.Run(tfs.name, func(t *testing.T) {
+			t.Parallel()
+
+			base, stateDir := tfs.open(t)
+			ltIdentity := writeLongTermKey(t, base, stateDir)
+
+			var versionDir string
+
+			checkVersionDir := func(string, string) error {
+				exists, err := afero.DirExists(base, versionDir)
+				require.NoError(t, err)
+
+				if exists {
+					assert.ElementsMatch(t,
+						[]string{"pub.age", "value.age", "priv.age", "metadata.age"},
+						dirNames(t, base, versionDir),
+						"version directory visible before it was complete")
+				}
+
+				return nil
+			}
+
+			fs := hookFs{Fs: base, before: checkVersionDir}
+			vault := &MockVersionVault{Name: testVaultName, fs: fs, stateDir: stateDir}
+			sv := secret.NewVersion(vault, "test/secret", "20231215.001")
+			versionDir = sv.Directory
+
+			value := memguard.NewBufferFromBytes([]byte("whole or nothing"))
+			defer value.Destroy()
+
+			require.NoError(t, sv.Save(value))
+			require.NoError(t, checkVersionDir("", ""))
+
+			got, err := sv.GetValue(ltIdentity)
+			require.NoError(t, err)
+
+			defer got.Destroy()
+
+			assert.Equal(t, "whole or nothing", got.String())
+		})
+	}
+}
+
+// TestVersionSaveFailureLeavesNothing makes the write of the encrypted
+// private key fail, after the value has been written, and checks that
+// neither the version nor its temporary directory is left behind.
+func TestVersionSaveFailureLeavesNothing(t *testing.T) {
+	t.Parallel()
+
+	for _, tfs := range testFilesystems {
+		t.Run(tfs.name, func(t *testing.T) {
+			t.Parallel()
+
+			base, stateDir := tfs.open(t)
+			writeLongTermKey(t, base, stateDir)
+
+			fs := hookFs{Fs: base, before: func(op, path string) error {
+				if op == opRename && filepath.Base(path) == "priv.age" {
+					return errInjected
+				}
+
+				return nil
+			}}
+			vault := &MockVersionVault{Name: testVaultName, fs: fs, stateDir: stateDir}
+			sv := secret.NewVersion(vault, "test/secret", "20231215.001")
+
+			value := memguard.NewBufferFromBytes([]byte("never stored"))
+			defer value.Destroy()
+
+			require.ErrorIs(t, sv.Save(value), errInjected)
+
+			// The secret directory holds only the empty versions directory
+			versionsDir := filepath.Dir(sv.Directory)
+			assert.Equal(t, []string{"versions"},
+				dirNames(t, base, filepath.Dir(versionsDir)))
+			assert.Empty(t, dirNames(t, base, versionsDir))
+		})
+	}
+}
+
+// TestSetCurrentVersionNeverMissing checks, before every change
+// SetCurrentVersion makes, that the current file exists: a reader or a crash
+// never finds the secret without a current version.
+func TestSetCurrentVersionNeverMissing(t *testing.T) {
+	t.Parallel()
+
+	for _, tfs := range testFilesystems {
+		t.Run(tfs.name, func(t *testing.T) {
+			t.Parallel()
+
+			base, dir := tfs.open(t)
+			secretDir := filepath.Join(dir, "secret")
+			require.NoError(t, base.MkdirAll(secretDir, 0o700))
+			require.NoError(t, secret.SetCurrentVersion(base, secretDir, "20231216.001"))
+
+			currentPath := filepath.Join(secretDir, currentFile)
+			fs := hookFs{Fs: base, before: func(string, string) error {
+				exists, err := afero.Exists(base, currentPath)
+				require.NoError(t, err)
+				assert.True(t, exists, "current is missing")
+
+				return nil
+			}}
+
+			require.NoError(t, secret.SetCurrentVersion(fs, secretDir, "20231216.002"))
+
+			version, err := secret.GetCurrentVersion(base, secretDir)
+			require.NoError(t, err)
+			assert.Equal(t, "20231216.002", version)
+		})
+	}
+}

internal/secret/keychainunlocker.go

@@ -195,7 +195,7 @@ func (k *KeychainUnlocker) Remove() error {
 
 	// Step 3: Remove directory
 	Debug("Removing keychain unlocker directory", "directory", k.Directory)
-	if err := k.fs.RemoveAll(k.Directory); err != nil {
+	if err := RemoveDirAtomic(k.fs, k.Directory); err != nil {
 		Debug("Failed to remove keychain unlocker directory", "error", err, "directory", k.Directory)
 
 		return fmt.Errorf("failed to remove keychain unlocker directory: %w", err)
@@ -373,7 +373,7 @@ func CreateKeychainUnlocker(fs afero.Fs, stateDir string) (*KeychainUnlocker, er
 	// Step 3: Store age recipient as plaintext
 	ageRecipient := ageIdentity.Recipient().String()
 	recipientPath := filepath.Join(unlockerDir, "pub.txt")
-	if err := afero.WriteFile(fs, recipientPath, []byte(ageRecipient), FilePerms); err != nil {
+	if err := WriteFileAtomic(fs, recipientPath, []byte(ageRecipient)); err != nil {
 		return nil, fmt.Errorf("failed to write age recipient: %w", err)
 	}
 
@@ -392,7 +392,7 @@ func CreateKeychainUnlocker(fs afero.Fs, stateDir string) (*KeychainUnlocker, er
 	}
 
 	agePrivKeyPath := filepath.Join(unlockerDir, "priv.age")
-	if err := afero.WriteFile(fs, agePrivKeyPath, encryptedAgePrivKey, FilePerms); err != nil {
+	if err := WriteFileAtomic(fs, agePrivKeyPath, encryptedAgePrivKey); err != nil {
 		return nil, fmt.Errorf("failed to write encrypted age private key: %w", err)
 	}
 
@@ -411,7 +411,7 @@ func CreateKeychainUnlocker(fs afero.Fs, stateDir string) (*KeychainUnlocker, er
 
 	// Write encrypted long-term private key
 	ltPrivKeyPath := filepath.Join(unlockerDir, "longterm.age")
-	if err := afero.WriteFile(fs, ltPrivKeyPath, encryptedLtPrivKeyToAge, FilePerms); err != nil {
+	if err := WriteFileAtomic(fs, ltPrivKeyPath, encryptedLtPrivKeyToAge); err != nil {
 		return nil, fmt.Errorf("failed to write encrypted long-term private key: %w", err)
 	}
 
@@ -451,9 +451,9 @@ func CreateKeychainUnlocker(fs afero.Fs, stateDir string) (*KeychainUnlocker, er
 		return nil, fmt.Errorf("failed to marshal unlocker metadata: %w", err)
 	}
 
-	if err := afero.WriteFile(fs,
+	if err := WriteFileAtomic(fs,
 		filepath.Join(unlockerDir, "unlocker-metadata.json"),
-		metadataBytes, FilePerms); err != nil {
+		metadataBytes); err != nil {
 		return nil, fmt.Errorf("failed to write unlocker metadata: %w", err)
 	}
 

internal/secret/passphraseunlocker.go

@@ -127,7 +127,7 @@ func (p *PassphraseUnlocker) Remove() error {
 
 	// For passphrase unlockers, we just need to remove the directory
 	// No external resources (like keychain items) to clean up
-	err := p.fs.RemoveAll(p.Directory)
+	err := RemoveDirAtomic(p.fs, p.Directory)
 	if err != nil {
 		return fmt.Errorf("failed to remove passphrase unlocker directory: %w", err)
 	}

internal/secret/pgpunlocker.go

@@ -172,7 +172,7 @@ func (p *PGPUnlocker) GetID() string {
 func (p *PGPUnlocker) Remove() error {
 	// For PGP unlockers, we just need to remove the directory
 	// No external resources (like keychain items) to clean up
-	err := p.fs.RemoveAll(p.Directory)
+	err := RemoveDirAtomic(p.fs, p.Directory)
 	if err != nil {
 		return fmt.Errorf("failed to remove PGP unlocker directory: %w", err)
 	}
@@ -275,7 +275,7 @@ func CreatePGPUnlocker(
 	ageRecipient := ageIdentity.Recipient().String()
 	recipientPath := filepath.Join(unlockerDir, "pub.txt")
 
-	err = afero.WriteFile(fs, recipientPath, []byte(ageRecipient), FilePerms)
+	err = WriteFileAtomic(fs, recipientPath, []byte(ageRecipient))
 	if err != nil {
 		return nil, fmt.Errorf("failed to write age recipient: %w", err)
 	}
@@ -298,7 +298,7 @@ func CreatePGPUnlocker(
 	// Write encrypted long-term private key
 	ltPrivKeyPath := filepath.Join(unlockerDir, "longterm.age")
 
-	err = afero.WriteFile(fs, ltPrivKeyPath, encryptedLtPrivKeyToAge, FilePerms)
+	err = WriteFileAtomic(fs, ltPrivKeyPath, encryptedLtPrivKeyToAge)
 	if err != nil {
 		return nil, fmt.Errorf("failed to write encrypted long-term private key: %w", err)
 	}
@@ -315,7 +315,7 @@ func CreatePGPUnlocker(
 
 	agePrivKeyPath := filepath.Join(unlockerDir, "priv.age.gpg")
 
-	err = afero.WriteFile(fs, agePrivKeyPath, encryptedAgePrivKey, FilePerms)
+	err = WriteFileAtomic(fs, agePrivKeyPath, encryptedAgePrivKey)
 	if err != nil {
 		return nil, fmt.Errorf("failed to write encrypted age private key: %w", err)
 	}
@@ -357,9 +357,8 @@ func writePGPUnlockerMetadata(
 		return nil, fmt.Errorf("failed to marshal unlocker metadata: %w", err)
 	}
 
-	err = afero.WriteFile(fs,
-		filepath.Join(unlockerDir, "unlocker-metadata.json"),
-		metadataBytes, FilePerms)
+	err = WriteFileAtomic(fs,
+		filepath.Join(unlockerDir, "unlocker-metadata.json"), metadataBytes)
 	if err != nil {
 		return nil, fmt.Errorf("failed to write unlocker metadata: %w", err)
 	}

internal/secret/seunlocker_darwin.go

@@ -148,7 +148,7 @@ func (s *SecureEnclaveUnlocker) Remove() error {
 	}
 
 	Debug("Removing SE unlocker directory", "directory", s.Directory)
-	if err := s.fs.RemoveAll(s.Directory); err != nil {
+	if err := RemoveDirAtomic(s.fs, s.Directory); err != nil {
 		return fmt.Errorf("failed to remove SE unlocker directory: %w", err)
 	}
 
@@ -271,7 +271,7 @@ func CreateSecureEnclaveUnlocker(
 
 	// Write SE-encrypted long-term key
 	ltKeyPath := filepath.Join(unlockerDir, seLongtermFilename)
-	if err := afero.WriteFile(fs, ltKeyPath, encryptedLtKey, FilePerms); err != nil {
+	if err := WriteFileAtomic(fs, ltKeyPath, encryptedLtKey); err != nil {
 		return nil, fmt.Errorf(
 			"failed to write SE-encrypted long-term key: %w",
 			err,
@@ -295,7 +295,7 @@ func CreateSecureEnclaveUnlocker(
 	}
 
 	metadataPath := filepath.Join(unlockerDir, "unlocker-metadata.json")
-	if err := afero.WriteFile(fs, metadataPath, metadataBytes, FilePerms); err != nil {
+	if err := WriteFileAtomic(fs, metadataPath, metadataBytes); err != nil {
 		return nil, fmt.Errorf("failed to write metadata: %w", err)
 	}
 

internal/secret/version.go

@@ -131,7 +131,10 @@ func GenerateVersionName(fs afero.Fs, secretDir string) (string, error) {
 	return fmt.Sprintf("%s.%03d", today, newSerial), nil
 }
 
-// Save saves the version metadata and value
+// Save saves the version metadata and value. The files are written into a
+// temporary directory that is renamed to sv.Directory once all of them are
+// complete, so the version directory is either whole or absent, even if the
+// process dies part-way.
 func (sv *Version) Save(value *memguard.LockedBuffer) error {
 	if value == nil {
 		return errNilValueBuffer
@@ -145,14 +148,22 @@ func (sv *Version) Save(value *memguard.LockedBuffer) error {
 
 	fs := sv.vault.GetFilesystem()
 
-	// Create version directory
-	err := fs.MkdirAll(sv.Directory, DirPerms)
+	// Create the versions directory the finished version is renamed into
+	err := fs.MkdirAll(filepath.Dir(sv.Directory), DirPerms)
 	if err != nil {
-		Debug("Failed to create version directory", "error", err, "dir", sv.Directory)
+		Debug("Failed to create versions directory", "error", err, "dir", sv.Directory)
 
-		return fmt.Errorf("failed to create version directory: %w", err)
+		return fmt.Errorf("failed to create versions directory: %w", err)
 	}
 
+	tmpDir, err := TempDirFor(fs, sv.Directory)
+	if err != nil {
+		return err
+	}
+
+	// Once the rename below has moved it into place, this finds nothing.
+	defer func() { _ = fs.RemoveAll(tmpDir) }()
+
 	// Generate a new keypair for this version
 	Debug("Generating version-specific keypair", "version", sv.Version)
 
@@ -173,21 +184,28 @@ func (sv *Version) Save(value *memguard.LockedBuffer) error {
 		slog.String("public_key", versionIdentity.Recipient().String()),
 	)
 
-	err = sv.writePublicKeyAndValue(fs, versionIdentity, value)
+	err = sv.writePublicKeyAndValue(fs, tmpDir, versionIdentity, value)
 	if err != nil {
 		return err
 	}
 
-	err = sv.writeEncryptedPrivateKey(fs, versionPrivateKeyBuffer)
+	err = sv.writeEncryptedPrivateKey(fs, tmpDir, versionPrivateKeyBuffer)
 	if err != nil {
 		return err
 	}
 
-	err = sv.writeEncryptedMetadata(fs, versionIdentity)
+	err = sv.writeEncryptedMetadata(fs, tmpDir, versionIdentity)
 	if err != nil {
 		return err
 	}
 
+	err = fs.Rename(tmpDir, sv.Directory)
+	if err != nil {
+		Debug("Failed to move version into place", "error", err, "dir", sv.Directory)
+
+		return fmt.Errorf("failed to move version into place: %w", err)
+	}
+
 	Debug("Successfully saved secret version",
 		"version", sv.Version, "secret_name", sv.SecretName)
 
@@ -358,17 +376,18 @@ func (sv *Version) GetValue(
 }
 
 // writePublicKeyAndValue stores the version's public key and the value
-// encrypted to it.
+// encrypted to it in dir.
 func (sv *Version) writePublicKeyAndValue(
 	fs afero.Fs,
+	dir string,
 	versionIdentity *age.X25519Identity,
 	value *memguard.LockedBuffer,
 ) error {
 	versionPublicKey := versionIdentity.Recipient().String()
-	pubKeyPath := filepath.Join(sv.Directory, "pub.age")
+	pubKeyPath := filepath.Join(dir, "pub.age")
 	Debug("Writing version public key", "path", pubKeyPath)
 
-	err := afero.WriteFile(fs, pubKeyPath, []byte(versionPublicKey), FilePerms)
+	err := WriteFileAtomic(fs, pubKeyPath, []byte(versionPublicKey))
 	if err != nil {
 		Debug("Failed to write version public key", "error", err, "path", pubKeyPath)
 
@@ -385,10 +404,10 @@ func (sv *Version) writePublicKeyAndValue(
 		return fmt.Errorf("failed to encrypt version value: %w", err)
 	}
 
-	valuePath := filepath.Join(sv.Directory, "value.age")
+	valuePath := filepath.Join(dir, "value.age")
 	Debug("Writing encrypted version value", "path", valuePath)
 
-	err = afero.WriteFile(fs, valuePath, encryptedValue, FilePerms)
+	err = WriteFileAtomic(fs, valuePath, encryptedValue)
 	if err != nil {
 		Debug("Failed to write encrypted version value", "error", err, "path", valuePath)
 
@@ -399,9 +418,10 @@ func (sv *Version) writePublicKeyAndValue(
 }
 
 // writeEncryptedPrivateKey encrypts the version's private key to the
-// vault's long-term public key and stores it.
+// vault's long-term public key and stores it in dir.
 func (sv *Version) writeEncryptedPrivateKey(
 	fs afero.Fs,
+	dir string,
 	versionPrivateKeyBuffer *memguard.LockedBuffer,
 ) error {
 	vaultDir, _ := sv.vault.GetDirectory()
@@ -435,10 +455,10 @@ func (sv *Version) writeEncryptedPrivateKey(
 		return fmt.Errorf("failed to encrypt version private key: %w", err)
 	}
 
-	privKeyPath := filepath.Join(sv.Directory, "priv.age")
+	privKeyPath := filepath.Join(dir, "priv.age")
 	Debug("Writing encrypted version private key", "path", privKeyPath)
 
-	err = afero.WriteFile(fs, privKeyPath, encryptedPrivKey, FilePerms)
+	err = WriteFileAtomic(fs, privKeyPath, encryptedPrivKey)
 	if err != nil {
 		Debug("Failed to write encrypted version private key",
 			"error", err, "path", privKeyPath)
@@ -450,9 +470,10 @@ func (sv *Version) writeEncryptedPrivateKey(
 }
 
 // writeEncryptedMetadata encrypts the version metadata to the version's
-// public key and stores it.
+// public key and stores it in dir.
 func (sv *Version) writeEncryptedMetadata(
 	fs afero.Fs,
+	dir string,
 	versionIdentity *age.X25519Identity,
 ) error {
 	Debug("Encrypting version metadata", "version", sv.Version)
@@ -476,10 +497,10 @@ func (sv *Version) writeEncryptedMetadata(
 		return fmt.Errorf("failed to encrypt version metadata: %w", err)
 	}
 
-	metadataPath := filepath.Join(sv.Directory, "metadata.age")
+	metadataPath := filepath.Join(dir, "metadata.age")
 	Debug("Writing encrypted version metadata", "path", metadataPath)
 
-	err = afero.WriteFile(fs, metadataPath, encryptedMetadata, FilePerms)
+	err = WriteFileAtomic(fs, metadataPath, encryptedMetadata)
 	if err != nil {
 		Debug("Failed to write encrypted version metadata",
 			"error", err, "path", metadataPath)
@@ -540,15 +561,12 @@ func GetCurrentVersion(fs afero.Fs, secretDir string) (string, error) {
 }
 
 // SetCurrentVersion updates the "current" file to point to a specific version
-// The file contains just the version name (e.g., "20231215.001")
+// The file contains just the version name (e.g., "20231215.001"). It is
+// replaced in one rename, so once written it always exists.
 func SetCurrentVersion(fs afero.Fs, secretDir string, version string) error {
 	currentPath := filepath.Join(secretDir, "current")
 
-	// Remove existing file if it exists
-	_ = fs.Remove(currentPath)
-
-	// Write just the version name to the file
-	err := afero.WriteFile(fs, currentPath, []byte(version), FilePerms)
+	err := WriteFileAtomic(fs, currentPath, []byte(version))
 	if err != nil {
 		return fmt.Errorf("failed to create current version file: %w", err)
 	}

internal/vault/errors.go

@@ -62,4 +62,10 @@ var (
 	// ErrUnlockerNotFound indicates no unlocker with the given ID exists.
 	// Composed as "unlocker with ID <id> not found".
 	ErrUnlockerNotFound = errors.New("not found")
+
+	// ErrNoLockForFilesystem indicates LockStateDir was given a filesystem
+	// it cannot lock. Composed as "cannot lock the state directory on
+	// filesystem <type>".
+	ErrNoLockForFilesystem = errors.New(
+		"cannot lock the state directory on filesystem")
 )

internal/vault/lock.go

@@ -0,0 +1,73 @@
+package vault
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+	"sync"
+	"syscall"
+
+	"git.eeqj.de/sneak/secret/internal/secret"
+	"github.com/spf13/afero"
+)
+
+// lockFileName is the file in the state directory that LockStateDir locks.
+const lockFileName = "lock"
+
+// memFsLock stands in for the lock file on the in-memory filesystem, which
+// has no file locks. Every in-memory filesystem in the process shares it.
+//
+//nolint:gochecknoglobals // must outlive the call that takes it
+var memFsLock sync.Mutex
+
+// LockStateDir takes the lock that a command changing anything under
+// stateDir holds until it returns, and returns the function that releases
+// it. While one command holds it, the next one waits here. Reads take no
+// lock: each file or directory a command changes is replaced in a single
+// rename, so a reader finds it as it was before or after, never half-made.
+//
+// On the real filesystem the lock is flock(2) on the file "lock" in
+// stateDir, which the kernel releases when the process dies, so a killed
+// command never leaves the tool locked. The in-memory filesystem the tests
+// use has no file locks, so a process-wide mutex stands in for flock there.
+// Any other filesystem is refused rather than left unlocked.
+func LockStateDir(fs afero.Fs, stateDir string) (func(), error) {
+	switch fs.(type) {
+	case *afero.OsFs:
+		return flockStateDir(stateDir)
+	case *afero.MemMapFs:
+		memFsLock.Lock()
+
+		return memFsLock.Unlock, nil
+	default:
+		return nil, fmt.Errorf("%w %T", ErrNoLockForFilesystem, fs)
+	}
+}
+
+// flockStateDir takes flock(2) on the lock file in stateDir, creating the
+// directory and the file if needed. Go opens files close-on-exec, so
+// programs the command runs, such as gpg, do not inherit the lock.
+func flockStateDir(stateDir string) (func(), error) {
+	err := os.MkdirAll(stateDir, secret.DirPerms)
+	if err != nil {
+		return nil, fmt.Errorf("failed to create state directory: %w", err)
+	}
+
+	lockPath := filepath.Join(stateDir, lockFileName)
+
+	//nolint:gosec // G304: the path is the lock file in the state directory
+	file, err := os.OpenFile(lockPath, os.O_RDWR|os.O_CREATE, secret.FilePerms)
+	if err != nil {
+		return nil, fmt.Errorf("failed to open lock file: %w", err)
+	}
+
+	err = syscall.Flock(int(file.Fd()), syscall.LOCK_EX)
+	if err != nil {
+		_ = file.Close()
+
+		return nil, fmt.Errorf("failed to lock %s: %w", lockPath, err)
+	}
+
+	// Closing the file releases the lock.
+	return func() { _ = file.Close() }, nil
+}

internal/vault/lock_test.go

@@ -0,0 +1,134 @@
+package vault_test
+
+import (
+	"testing"
+	"time"
+
+	"git.eeqj.de/sneak/secret/internal/vault"
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+const (
+	// lockWait is how long a test waits for the lock before deciding it
+	// will never come free.
+	lockWait = 10 * time.Second
+
+	// heldWait is how long a test watches a second holder fail to take a
+	// lock that is held. Broken exclusion lets it in at once.
+	heldWait = 100 * time.Millisecond
+)
+
+// lockFilesystem is a filesystem LockStateDir can lock, with a state
+// directory on it.
+type lockFilesystem struct {
+	name     string
+	fs       afero.Fs
+	stateDir string
+}
+
+// lockFilesystems returns the real filesystem, locked with flock, and the
+// in-memory one, locked with a mutex.
+func lockFilesystems(t *testing.T) []lockFilesystem {
+	t.Helper()
+
+	return []lockFilesystem{
+		{"memory", afero.NewMemMapFs(), testStateDir},
+		{"real", afero.NewOsFs(), t.TempDir()},
+	}
+}
+
+// lockInBackground starts taking the lock and returns a channel that
+// delivers the function releasing it once it has been taken.
+func lockInBackground(
+	t *testing.T, fs afero.Fs, stateDir string,
+) <-chan func() {
+	t.Helper()
+
+	taken := make(chan func(), 1)
+
+	go func() {
+		release, err := vault.LockStateDir(fs, stateDir)
+		if assert.NoError(t, err) {
+			taken <- release
+		}
+	}()
+
+	return taken
+}
+
+// TestLockStateDirExcludes checks that while the lock is held a second
+// holder, with its own open lock file on the real filesystem, waits, and
+// that it gets the lock once the first releases it.
+func TestLockStateDirExcludes(t *testing.T) {
+	t.Parallel()
+
+	for _, lfs := range lockFilesystems(t) {
+		t.Run(lfs.name, func(t *testing.T) {
+			t.Parallel()
+
+			release, err := vault.LockStateDir(lfs.fs, lfs.stateDir)
+			require.NoError(t, err)
+
+			taken := lockInBackground(t, lfs.fs, lfs.stateDir)
+
+			select {
+			case second := <-taken:
+				second()
+				release()
+				t.Fatal("a second holder took the lock while it was held")
+			case <-time.After(heldWait):
+			}
+
+			release()
+
+			select {
+			case second := <-taken:
+				second()
+			case <-time.After(lockWait):
+				t.Fatal("the second holder never got the lock")
+			}
+		})
+	}
+}
+
+// TestLockStateDirFreeAfterPanic checks that a holder that panics, and
+// releases the lock with defer as every command does, leaves it free.
+func TestLockStateDirFreeAfterPanic(t *testing.T) {
+	t.Parallel()
+
+	for _, lfs := range lockFilesystems(t) {
+		t.Run(lfs.name, func(t *testing.T) {
+			t.Parallel()
+
+			assert.Panics(t, func() {
+				release, err := vault.LockStateDir(lfs.fs, lfs.stateDir)
+				require.NoError(t, err)
+
+				defer release()
+
+				panic("the command failed")
+			})
+
+			select {
+			case release := <-lockInBackground(t, lfs.fs, lfs.stateDir):
+				release()
+			case <-time.After(lockWait):
+				t.Fatal("the lock was still held after its holder panicked")
+			}
+		})
+	}
+}
+
+// TestLockStateDirRefusesOtherFilesystems checks that a filesystem with no
+// lock implementation is refused instead of being used unlocked.
+func TestLockStateDirRefusesOtherFilesystems(t *testing.T) {
+	t.Parallel()
+
+	fs := afero.NewReadOnlyFs(afero.NewMemMapFs())
+
+	release, err := vault.LockStateDir(fs, testStateDir)
+	require.ErrorIs(t, err, vault.ErrNoLockForFilesystem)
+	assert.Nil(t, release)
+}

internal/vault/management.go

@@ -169,7 +169,7 @@ func processMnemonicForVault(
 
 	ltPubKeyPath := filepath.Join(vaultDir, "pub.age")
 
-	err = afero.WriteFile(fs, ltPubKeyPath, []byte(ltPubKey), secret.FilePerms)
+	err = secret.WriteFileAtomic(fs, ltPubKeyPath, []byte(ltPubKey))
 	if err != nil {
 		return 0, "", "", fmt.Errorf("failed to write long-term public key: %w", err)
 	}
@@ -295,21 +295,13 @@ func SelectVault(fs afero.Fs, stateDir string, name string) error {
 		return fmt.Errorf("vault %s %w", name, ErrVaultNotFound)
 	}
 
-	// Create or update the currentvault file with just the vault name
+	// Create or replace the currentvault file with just the vault name. It
+	// is replaced in one rename, so it never goes missing.
 	currentVaultPath := filepath.Join(stateDir, "currentvault")
 
-	// Remove existing file if it exists
-	_, err = fs.Stat(currentVaultPath)
-	if err == nil {
-		secret.Debug("Removing existing currentvault file", "path", currentVaultPath)
-
-		_ = fs.Remove(currentVaultPath)
-	}
-
-	// Write just the vault name to the file
 	secret.Debug("Writing currentvault file", "vault_name", name)
 
-	err = afero.WriteFile(fs, currentVaultPath, []byte(name), secret.FilePerms)
+	err = secret.WriteFileAtomic(fs, currentVaultPath, []byte(name))
 	if err != nil {
 		return fmt.Errorf("failed to select vault: %w", err)
 	}

internal/vault/metadata.go

@@ -113,7 +113,7 @@ func SaveVaultMetadata(fs afero.Fs, vaultDir string, metadata *Metadata) error {
 		return fmt.Errorf("failed to marshal vault metadata: %w", err)
 	}
 
-	err = afero.WriteFile(fs, metadataPath, metadataBytes, secret.FilePerms)
+	err = secret.WriteFileAtomic(fs, metadataPath, metadataBytes)
 	if err != nil {
 		return fmt.Errorf("failed to write vault metadata: %w", err)
 	}

internal/vault/secrets.go

@@ -156,17 +156,59 @@ func (v *Vault) AddSecret(name string, value *memguard.LockedBuffer, force bool)
 		slog.String("secret_dir", secretDir),
 	)
 
-	// Check for an existing secret and prepare its directory
-	exists, previousVersion, err := v.prepareSecretDir(name, secretDir, force)
+	// Check for an existing secret and the version the new one supersedes
+	exists, previousVersion, err := v.checkExistingSecret(name, secretDir, force)
 	if err != nil {
 		return err
 	}
 
+	if exists {
+		return v.addVersion(name, secretDir, value, previousVersion)
+	}
+
+	return v.addNewSecret(name, secretDir, value)
+}
+
+// addNewSecret creates a secret by assembling its first version and current
+// pointer in a temporary directory, then renaming that directory to
+// secretDir, so an interrupted add leaves no half-made secret behind.
+func (v *Vault) addNewSecret(
+	name, secretDir string, value *memguard.LockedBuffer,
+) error {
+	buildDir, err := secret.TempDirFor(v.fs, secretDir)
+	if err != nil {
+		return err
+	}
+
+	// Once the rename below has moved it into place, this finds nothing.
+	defer func() { _ = v.fs.RemoveAll(buildDir) }()
+
+	err = v.addVersion(name, buildDir, value, nil)
+	if err != nil {
+		return err
+	}
+
+	err = v.fs.Rename(buildDir, secretDir)
+	if err != nil {
+		return fmt.Errorf("failed to move new secret into place: %w", err)
+	}
+
+	return nil
+}
+
+// addVersion saves value as a new version under secretDir, sets the
+// notAfter timestamp of the version it supersedes, if any, and then points
+// current at the new version. Until that last step, current still names the
+// previous version, which stays readable.
+func (v *Vault) addVersion(
+	name, secretDir string, value *memguard.LockedBuffer,
+	previousVersion *secret.Version,
+) error {
 	now := time.Now()
 
 	// Create the new version and save the encrypted value
 	versionName, err := v.createAndSaveVersion(
-		name, secretDir, value, previousVersion, &now, exists)
+		name, secretDir, value, previousVersion, &now)
 	if err != nil {
 		return err
 	}
@@ -236,7 +278,7 @@ func updateVersionMetadata(
 	// Write encrypted metadata
 	metadataPath := filepath.Join(version.Directory, "metadata.age")
 
-	err = afero.WriteFile(fs, metadataPath, encryptedMetadata, secret.FilePerms)
+	err = secret.WriteFileAtomic(fs, metadataPath, encryptedMetadata)
 	if err != nil {
 		return fmt.Errorf("failed to write encrypted version metadata: %w", err)
 	}
@@ -394,12 +436,14 @@ func (v *Vault) GetSecretObject(name string) (*secret.Secret, error) {
 	return secretObj, nil
 }
 
-// CopySecretVersion copies a single version from source to this vault
-// It decrypts the value using srcIdentity and re-encrypts for this vault
+// CopySecretVersion copies a single version from source into destSecretDir
+// in this vault. It decrypts the value using srcIdentity and re-encrypts
+// for this vault.
 func (v *Vault) CopySecretVersion(
 	srcVersion *secret.Version,
 	srcIdentity *age.X25519Identity,
 	destSecretName string,
+	destSecretDir string,
 	destVersionName string,
 ) error {
 	secret.DebugWith("Copying secret version to vault",
@@ -425,6 +469,7 @@ func (v *Vault) CopySecretVersion(
 
 	// Create destination version with same name
 	destVersion := secret.NewVersion(v, destSecretName, destVersionName)
+	destVersion.Directory = filepath.Join(destSecretDir, "versions", destVersionName)
 
 	// Copy metadata (preserve original timestamps)
 	destVersion.Metadata = srcVersion.Metadata
@@ -465,11 +510,11 @@ func (v *Vault) CopySecretAllVersions(
 		return fmt.Errorf("failed to get destination vault directory: %w", err)
 	}
 
-	// Check if destination secret already exists and clear it if forced
+	// Refuse to replace an existing destination secret unless forced
 	destStorageName := strings.ReplaceAll(destSecretName, "/", "%")
 	destSecretDir := filepath.Join(destVaultDir, "secrets.d", destStorageName)
 
-	err = v.prepareCopyDestination(destSecretDir, destSecretName, force)
+	err = v.checkCopyDestination(destSecretDir, destSecretName, force)
 	if err != nil {
 		return err
 	}
@@ -505,14 +550,8 @@ func (v *Vault) CopySecretAllVersions(
 		return fmt.Errorf("failed to get current version: %w", err)
 	}
 
-	// Create destination secret directory
-	err = v.fs.MkdirAll(destSecretDir, secret.DirPerms)
-	if err != nil {
-		return fmt.Errorf("failed to create destination secret directory: %w", err)
-	}
-
-	// Copy each version and set the current pointer, rolling back on error
-	err = v.copyVersionsWithRollback(srcVault, srcIdentity,
+	// Copy each version and the current pointer, then move the copy into place
+	err = v.copyVersions(srcVault, srcIdentity,
 		srcSecretName, destSecretName, destSecretDir, versions, currentVersion)
 	if err != nil {
 		return err
@@ -527,10 +566,10 @@ func (v *Vault) CopySecretAllVersions(
 	return nil
 }
 
-// prepareSecretDir checks for an existing secret directory and prepares it
-// for a new version. It returns whether the secret already existed and the
-// current version to be superseded, if any.
-func (v *Vault) prepareSecretDir(
+// checkExistingSecret reports whether the secret already exists, refuses to
+// overwrite it unless force is set, and returns its current version, which
+// the new version supersedes, if any.
+func (v *Vault) checkExistingSecret(
 	name, secretDir string, force bool,
 ) (bool, *secret.Version, error) {
 	// Check if secret already exists
@@ -547,19 +586,6 @@ func (v *Vault) prepareSecretDir(
 	secret.Debug("Secret existence check complete", "exists", exists)
 
 	if !exists {
-		// Create secret directory for new secret
-		secret.Debug("Creating secret directory", "secret_dir", secretDir)
-
-		err = v.fs.MkdirAll(secretDir, secret.DirPerms)
-		if err != nil {
-			secret.Debug("Failed to create secret directory",
-				"error", err, "secret_dir", secretDir)
-
-			return false, nil, fmt.Errorf("failed to create secret directory: %w", err)
-		}
-
-		secret.Debug("Created secret directory successfully")
-
 		return false, nil, nil
 	}
 
@@ -701,11 +727,11 @@ func (v *Vault) resolveSecretVersion(name, version string) (string, error) {
 }
 
 // createAndSaveVersion generates a new version name, sets the version
-// timestamps, and saves the encrypted value. When saving fails for a newly
-// created secret, the secret directory is removed again.
+// timestamps, and saves the encrypted value under secretDir, which is a
+// temporary directory while a new secret is being assembled.
 func (v *Vault) createAndSaveVersion(
 	name, secretDir string, value *memguard.LockedBuffer,
-	previousVersion *secret.Version, now *time.Time, exists bool,
+	previousVersion *secret.Version, now *time.Time,
 ) (string, error) {
 	// Generate new version name
 	versionName, err := secret.GenerateVersionName(v.fs, secretDir)
@@ -719,6 +745,7 @@ func (v *Vault) createAndSaveVersion(
 
 	// Create new version
 	newVersion := secret.NewVersion(v, name, versionName)
+	newVersion.Directory = filepath.Join(secretDir, "versions", versionName)
 
 	// Set version timestamps
 	if previousVersion == nil {
@@ -738,57 +765,73 @@ func (v *Vault) createAndSaveVersion(
 	if err != nil {
 		secret.Debug("Failed to save new version", "error", err, "version", versionName)
 
-		// Clean up the secret directory if this was a new secret
-		if !exists {
-			secret.Debug("Cleaning up secret directory due to save failure",
-				"secret_dir", secretDir)
-
-			_ = v.fs.RemoveAll(secretDir)
-		}
-
 		return "", fmt.Errorf("failed to save version: %w", err)
 	}
 
 	return versionName, nil
 }
 
-// copyVersionsWithRollback copies each version of the source secret into the
-// destination directory and sets the current version pointer, removing the
-// partial copy when any step fails.
-func (v *Vault) copyVersionsWithRollback(
+// copyVersions copies each version of the source secret and its current
+// pointer into a temporary directory, then moves that directory to
+// destSecretDir, replacing a secret already there. Nothing in this vault
+// changes until the copy is complete, so an interrupted copy leaves only a
+// temporary directory behind.
+func (v *Vault) copyVersions(
 	srcVault *Vault, srcIdentity *age.X25519Identity,
 	srcSecretName, destSecretName, destSecretDir string,
 	versions []string, currentVersion string,
 ) error {
-	// Copy each version
+	buildDir, err := secret.TempDirFor(v.fs, destSecretDir)
+	if err != nil {
+		return err
+	}
+
+	// Once the rename below has moved it into place, this finds nothing.
+	defer func() { _ = v.fs.RemoveAll(buildDir) }()
+
 	for _, versionName := range versions {
 		srcVersion := secret.NewVersion(srcVault, srcSecretName, versionName)
 
-		err := v.CopySecretVersion(srcVersion, srcIdentity, destSecretName, versionName)
+		err = v.CopySecretVersion(
+			srcVersion, srcIdentity, destSecretName, buildDir, versionName)
 		if err != nil {
-			// Rollback: remove partial copy
-			secret.Debug("Rolling back partial copy due to error", "error", err)
-
-			_ = v.fs.RemoveAll(destSecretDir)
-
 			return fmt.Errorf("failed to copy version %s: %w", versionName, err)
 		}
 	}
 
-	// Set current version
-	err := secret.SetCurrentVersion(v.fs, destSecretDir, currentVersion)
+	err = secret.SetCurrentVersion(v.fs, buildDir, currentVersion)
 	if err != nil {
-		_ = v.fs.RemoveAll(destSecretDir)
-
 		return fmt.Errorf("failed to set current version: %w", err)
 	}
 
+	// With --force, the secret being replaced goes only now that its
+	// replacement is complete
+	exists, err := afero.DirExists(v.fs, destSecretDir)
+	if err != nil {
+		return fmt.Errorf("failed to check destination: %w", err)
+	}
+
+	if exists {
+		secret.Debug("Removing existing destination secret", "path", destSecretDir)
+
+		err = secret.RemoveDirAtomic(v.fs, destSecretDir)
+		if err != nil {
+			return fmt.Errorf("failed to remove existing destination secret: %w", err)
+		}
+	}
+
+	err = v.fs.Rename(buildDir, destSecretDir)
+	if err != nil {
+		return fmt.Errorf("failed to move copied secret into place: %w", err)
+	}
+
 	return nil
 }
 
-// prepareCopyDestination ensures the destination secret directory can be
-// created, removing an existing secret when force is set.
-func (v *Vault) prepareCopyDestination(
+// checkCopyDestination refuses to copy over an existing secret unless force
+// is set. A secret being replaced is removed by copyVersions, once its
+// replacement is complete.
+func (v *Vault) checkCopyDestination(
 	destSecretDir, destSecretName string, force bool,
 ) error {
 	exists, err := afero.DirExists(v.fs, destSecretDir)
@@ -803,15 +846,5 @@ func (v *Vault) prepareCopyDestination(
 		)
 	}
 
-	if exists && force {
-		// Remove existing secret
-		secret.Debug("Removing existing destination secret", "path", destSecretDir)
-
-		err = v.fs.RemoveAll(destSecretDir)
-		if err != nil {
-			return fmt.Errorf("failed to remove existing destination secret: %w", err)
-		}
-	}
-
 	return nil
 }

internal/vault/unlockers.go

@@ -310,30 +310,16 @@ func (v *Vault) SelectUnlocker(unlockerID string) error {
 		return fmt.Errorf("unlocker with ID %s %w", unlockerID, ErrUnlockerNotFound)
 	}
 
-	// Create/update current-unlocker file with just the unlocker name
+	// Create or replace the current-unlocker file with just the unlocker
+	// name. It is replaced in one rename, so it never goes missing.
 	currentUnlockerPath := filepath.Join(vaultDir, "current-unlocker")
 
-	// Remove existing file if it exists
-	exists, err := afero.Exists(v.fs, currentUnlockerPath)
-	if err != nil {
-		return fmt.Errorf("failed to check if current-unlocker file exists: %w", err)
-	}
-
-	if exists {
-		err = v.fs.Remove(currentUnlockerPath)
-		if err != nil {
-			return fmt.Errorf("failed to remove existing current-unlocker file: %w", err)
-		}
-	}
-
 	// Get just the unlocker name (basename of the directory)
 	unlockerName := filepath.Base(targetUnlockerDir)
 
-	// Write just the unlocker name to the file
 	secret.Debug("Writing current-unlocker file", "unlocker_name", unlockerName)
 
-	err = afero.WriteFile(v.fs, currentUnlockerPath, []byte(unlockerName),
-		secret.FilePerms)
+	err = secret.WriteFileAtomic(v.fs, currentUnlockerPath, []byte(unlockerName))
 	if err != nil {
 		return fmt.Errorf("failed to create current-unlocker file: %w", err)
 	}
@@ -351,6 +337,14 @@ func (v *Vault) CreatePassphraseUnlocker(
 		return nil, fmt.Errorf("failed to get vault directory: %w", err)
 	}
 
+	// We need to get the long-term key (either from memory if unlocked, or
+	// derive it). Getting it before anything is written means failing to
+	// get it changes nothing, even when replacing the current unlocker.
+	ltIdentity, err := v.GetOrDeriveLongTermKey()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get long-term key: %w", err)
+	}
+
 	// Create unlocker directory
 	unlockerDir := filepath.Join(vaultDir, "unlockers.d", unlockerTypePassphrase)
 
@@ -371,33 +365,7 @@ func (v *Vault) CreatePassphraseUnlocker(
 		return nil, err
 	}
 
-	// Create metadata
-	metadata := UnlockerMetadata{
-		Type:      unlockerTypePassphrase,
-		CreatedAt: time.Now(),
-		Flags:     []string{},
-	}
-
-	// Write metadata
-	metadataBytes, err := json.MarshalIndent(metadata, "", "  ")
-	if err != nil {
-		return nil, fmt.Errorf("failed to marshal metadata: %w", err)
-	}
-
-	metadataPath := filepath.Join(unlockerDir, "unlocker-metadata.json")
-
-	err = afero.WriteFile(v.fs, metadataPath, metadataBytes, secret.FilePerms)
-	if err != nil {
-		return nil, fmt.Errorf("failed to write unlocker metadata: %w", err)
-	}
-
 	// Encrypt long-term private key to this unlocker
-	// We need to get the long-term key (either from memory if unlocked, or derive it)
-	ltIdentity, err := v.GetOrDeriveLongTermKey()
-	if err != nil {
-		return nil, fmt.Errorf("failed to get long-term key: %w", err)
-	}
-
 	ltPrivKeyBuffer := memguard.NewBufferFromBytes([]byte(ltIdentity.String()))
 	defer ltPrivKeyBuffer.Destroy()
 
@@ -409,11 +377,31 @@ func (v *Vault) CreatePassphraseUnlocker(
 
 	ltPrivKeyPath := filepath.Join(unlockerDir, "longterm.age")
 
-	err = afero.WriteFile(v.fs, ltPrivKeyPath, encryptedLtPrivKey, secret.FilePerms)
+	err = secret.WriteFileAtomic(v.fs, ltPrivKeyPath, encryptedLtPrivKey)
 	if err != nil {
 		return nil, fmt.Errorf("failed to write encrypted long-term private key: %w", err)
 	}
 
+	// Write the metadata last: readers skip an unlocker directory without
+	// it, so an unlocker interrupted before this point is never used.
+	metadata := UnlockerMetadata{
+		Type:      unlockerTypePassphrase,
+		CreatedAt: time.Now(),
+		Flags:     []string{},
+	}
+
+	metadataBytes, err := json.MarshalIndent(metadata, "", "  ")
+	if err != nil {
+		return nil, fmt.Errorf("failed to marshal metadata: %w", err)
+	}
+
+	metadataPath := filepath.Join(unlockerDir, "unlocker-metadata.json")
+
+	err = secret.WriteFileAtomic(v.fs, metadataPath, metadataBytes)
+	if err != nil {
+		return nil, fmt.Errorf("failed to write unlocker metadata: %w", err)
+	}
+
 	// Create the unlocker instance
 	unlocker := secret.NewPassphraseUnlocker(v.fs, unlockerDir, metadata)
 
@@ -467,9 +455,8 @@ func (v *Vault) writeUnlockerKeypair(
 	// Write public key
 	pubKeyPath := filepath.Join(unlockerDir, "pub.age")
 
-	err := afero.WriteFile(v.fs, pubKeyPath,
-		[]byte(unlockerIdentity.Recipient().String()),
-		secret.FilePerms)
+	err := secret.WriteFileAtomic(v.fs, pubKeyPath,
+		[]byte(unlockerIdentity.Recipient().String()))
 	if err != nil {
 		return fmt.Errorf("failed to write unlocker public key: %w", err)
 	}
@@ -488,7 +475,7 @@ func (v *Vault) writeUnlockerKeypair(
 	// Write encrypted private key
 	privKeyPath := filepath.Join(unlockerDir, "priv.age")
 
-	err = afero.WriteFile(v.fs, privKeyPath, encryptedPrivKey, secret.FilePerms)
+	err = secret.WriteFileAtomic(v.fs, privKeyPath, encryptedPrivKey)
 	if err != nil {
 		return fmt.Errorf("failed to write encrypted unlocker private key: %w", err)
 	}

internal/vault/vault_error_test.go

@@ -90,4 +90,10 @@ func TestAddSecretCleansUpOnFailure(t *testing.T) {
 	secretDir := filepath.Join(vaultDir, "secrets.d", testSecretName)
 	exists, _ := afero.DirExists(fs, secretDir)
 	assert.False(t, exists, "Secret directory should not exist after failed AddSecret")
+
+	// Nor is the temporary directory the secret was assembled in left behind
+	entries, err := afero.ReadDir(fs, vaultDir)
+	require.NoError(t, err)
+	require.Len(t, entries, 1)
+	assert.Equal(t, "pub.age", entries[0].Name())
 }