Leave remote info orphan figures unknown when a manifest is unreadable (closes #228)

When a manifest could not be read, remote info skipped it, counted that
snapshot's blobs as orphaned and advised running prune. The orphan
figures are now unknown in that case, with no prune advice; --json gives
them as null and lists the unreadable remote keys in
unreadable_manifests.

Names under metadata/ were used unchecked and printed raw. A name that
is not a remote key is now skipped with a warning. Its manifest is then
not read either, so a skipped name also leaves the orphan figures
unknown; --json counts such names in skipped_metadata_names without
printing them.

The closing log line carries the unreadable manifest count in place of
the orphan count.

Model: opus-5-5

README.md

@@ -390,9 +390,12 @@ recipients, and local database statistics.
 
 **`remote info`**: Show storage backend type and location plus detailed
 remote storage inventory: per-snapshot metadata sizes, blob counts, and
-orphaned blob detection. If a manifest cannot be read, the orphaned blob
-figures are reported as unknown; `--json` gives them as `null` and lists
-the remote key of each unreadable manifest in `unreadable_manifests`.
+orphaned blob detection. A name under `metadata/` that is not a remote
+key is skipped with a warning and is not printed. If a manifest cannot be
+read, or a name was skipped, the orphaned blob figures are reported as
+unknown; `--json` gives them as `null`, lists the remote key of each
+unreadable manifest in `unreadable_manifests` and counts the skipped
+names in `skipped_metadata_names`.
 * `--json`: Output as JSON
 
 **`remote nuke`**: Delete every snapshot's metadata and every blob from the

TODO.md

@@ -32,7 +32,19 @@ the tag exists and is exercised; what is left is merging `next` to
   advice, and `--json` gives them as `null` with the unreadable remote
   keys in `unreadable_manifests`. A name under `metadata/` that is not
   64 lowercase hex characters is now skipped with a warning instead of
-  being printed, control characters included.
+  being printed, control characters included. Its manifest is then not
+  read either, so a skipped name also leaves the orphan figures unknown,
+  and `--json` counts such names in `skipped_metadata_names`.
+
+- 2026-10-07: Made a backup notice a file rewritten with its size
+  unchanged and a new mtime in the same second as the one in the index
+  ([issue #226](https://git.eeqj.de/sneak/vaultik/issues/226)). The
+  `files` table held mtime in whole seconds and the scanner compared
+  whole seconds, so every later snapshot kept the old content. A new
+  `mtime_nsec` column holds the nanoseconds within the second that
+  `mtime` holds, and the scanner compares the full mtime. A local index
+  created before the change lacks the column and is rebuilt with
+  `vaultik database delete` and a full backup.
 
 - 2026-10-07: Made taking the process-wide lock atomic
   ([issue #227](https://git.eeqj.de/sneak/vaultik/issues/227)). The lock

docs/DATAMODEL.md

@@ -36,7 +36,8 @@ Stores metadata about files in the filesystem being backed up.
 **Columns:**
 - `id` (TEXT PRIMARY KEY) - UUID for the file record
 - `path` (TEXT NOT NULL UNIQUE) - Absolute file path
-- `mtime` (INTEGER NOT NULL) - Modification time as Unix timestamp
+- `mtime` (INTEGER NOT NULL) - Modification time, whole seconds since the Unix epoch
+- `mtime_nsec` (INTEGER NOT NULL) - Nanoseconds within that second, 0 to 999999999
 - `size` (INTEGER NOT NULL) - File size in bytes
 - `mode` (INTEGER NOT NULL) - Unix file permissions and type
 - `uid` (INTEGER NOT NULL) - User ID of file owner

internal/database/files.go

@@ -33,11 +33,13 @@ func (r *FileRepository) Create(ctx context.Context, tx *sql.Tx, file *File) err
 	}
 
 	query := `
-		INSERT INTO files (id, path, source_path, mtime, size, mode, uid, gid, link_target)
-		VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+		INSERT INTO files
+			(id, path, source_path, mtime, mtime_nsec, size, mode, uid, gid, link_target)
+		VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
 		ON CONFLICT(path) DO UPDATE SET
 			source_path = excluded.source_path,
 			mtime = excluded.mtime,
+			mtime_nsec = excluded.mtime_nsec,
 			size = excluded.size,
 			mode = excluded.mode,
 			uid = excluded.uid,
@@ -54,16 +56,19 @@ func (r *FileRepository) Create(ctx context.Context, tx *sql.Tx, file *File) err
 	if tx != nil {
 		LogSQL("Execute", query,
 			file.ID.String(), file.Path.String(), file.SourcePath.String(),
-			file.MTime.Unix(), file.Size, file.Mode, file.UID, file.GID,
+			file.MTime.Unix(), file.MTime.Nanosecond(),
+			file.Size, file.Mode, file.UID, file.GID,
 			file.LinkTarget.String())
 		err = tx.QueryRowContext(ctx, query,
 			file.ID.String(), file.Path.String(), file.SourcePath.String(),
-			file.MTime.Unix(), file.Size, file.Mode, file.UID, file.GID,
+			file.MTime.Unix(), file.MTime.Nanosecond(),
+			file.Size, file.Mode, file.UID, file.GID,
 			file.LinkTarget.String()).Scan(&idStr)
 	} else {
 		err = r.db.QueryRowWithLog(ctx, query,
 			file.ID.String(), file.Path.String(), file.SourcePath.String(),
-			file.MTime.Unix(), file.Size, file.Mode, file.UID, file.GID,
+			file.MTime.Unix(), file.MTime.Nanosecond(),
+			file.Size, file.Mode, file.UID, file.GID,
 			file.LinkTarget.String()).Scan(&idStr)
 	}
 
@@ -84,7 +89,7 @@ func (r *FileRepository) Create(ctx context.Context, tx *sql.Tx, file *File) err
 // in the index.
 func (r *FileRepository) GetByPath(ctx context.Context, path string) (*File, error) {
 	query := `
-		SELECT id, path, source_path, mtime, size, mode, uid, gid, link_target
+		SELECT id, path, source_path, mtime, mtime_nsec, size, mode, uid, gid, link_target
 		FROM files
 		WHERE path = ?
 	`
@@ -104,7 +109,7 @@ func (r *FileRepository) GetByPath(ctx context.Context, path string) (*File, err
 // GetByID retrieves a file by its UUID
 func (r *FileRepository) GetByID(ctx context.Context, id types.FileID) (*File, error) {
 	query := `
-		SELECT id, path, source_path, mtime, size, mode, uid, gid, link_target
+		SELECT id, path, source_path, mtime, mtime_nsec, size, mode, uid, gid, link_target
 		FROM files
 		WHERE id = ?
 	`
@@ -127,7 +132,7 @@ func (r *FileRepository) GetByPathTx(
 	ctx context.Context, tx *sql.Tx, path string,
 ) (*File, error) {
 	query := `
-		SELECT id, path, source_path, mtime, size, mode, uid, gid, link_target
+		SELECT id, path, source_path, mtime, mtime_nsec, size, mode, uid, gid, link_target
 		FROM files
 		WHERE path = ?
 	`
@@ -158,13 +163,14 @@ func (r *FileRepository) ListModifiedSince(
 	ctx context.Context, since time.Time,
 ) ([]*File, error) {
 	query := `
-		SELECT id, path, source_path, mtime, size, mode, uid, gid, link_target
+		SELECT id, path, source_path, mtime, mtime_nsec, size, mode, uid, gid, link_target
 		FROM files
-		WHERE mtime >= ?
+		WHERE (mtime, mtime_nsec) >= (?, ?)
 		ORDER BY path
 	`
 
-	rows, err := r.db.conn.QueryContext(ctx, query, since.Unix())
+	rows, err := r.db.conn.QueryContext(ctx, query,
+		since.Unix(), since.Nanosecond())
 	if err != nil {
 		return nil, fmt.Errorf("querying files: %w", err)
 	}
@@ -239,7 +245,7 @@ func (r *FileRepository) ListUnderPath(
 
 	// LIKE would ignore ASCII case and treat _ and % in path as wildcards.
 	query := `
-		SELECT id, path, source_path, mtime, size, mode, uid, gid, link_target
+		SELECT id, path, source_path, mtime, mtime_nsec, size, mode, uid, gid, link_target
 		FROM files
 		WHERE path = ? OR substr(path, 1, length(?)) = ?
 		ORDER BY path
@@ -324,7 +330,7 @@ func (r *FileRepository) ListIDsWithChunksNotInUploadedBlobs(
 // ListAll returns all files in the database
 func (r *FileRepository) ListAll(ctx context.Context) ([]*File, error) {
 	query := `
-		SELECT id, path, source_path, mtime, size, mode, uid, gid, link_target
+		SELECT id, path, source_path, mtime, mtime_nsec, size, mode, uid, gid, link_target
 		FROM files
 		ORDER BY path
 	`
@@ -365,7 +371,7 @@ func (r *FileRepository) CreateBatch(
 	}
 
 	// Each files row binds this many SQL variables.
-	const fileCols = 9
+	const fileCols = 10
 
 	// Batch at 100 rows to be safe with SQLite's variable limit.
 	const batchSize = 100
@@ -376,7 +382,7 @@ func (r *FileRepository) CreateBatch(
 		batch := files[i:end]
 
 		query := `INSERT INTO files
-			(id, path, source_path, mtime, size, mode, uid, gid, link_target)
+			(id, path, source_path, mtime, mtime_nsec, size, mode, uid, gid, link_target)
 			VALUES `
 
 		args := make([]any, 0, len(batch)*fileCols)
@@ -388,11 +394,12 @@ func (r *FileRepository) CreateBatch(
 				querySb325.WriteString(", ")
 			}
 
-			querySb325.WriteString("(?, ?, ?, ?, ?, ?, ?, ?, ?)")
+			querySb325.WriteString("(?, ?, ?, ?, ?, ?, ?, ?, ?, ?)")
 
 			args = append(args,
 				f.ID.String(), f.Path.String(), f.SourcePath.String(),
-				f.MTime.Unix(), f.Size, f.Mode, f.UID, f.GID,
+				f.MTime.Unix(), f.MTime.Nanosecond(),
+				f.Size, f.Mode, f.UID, f.GID,
 				f.LinkTarget.String())
 		}
 
@@ -401,6 +408,7 @@ func (r *FileRepository) CreateBatch(
 		query += ` ON CONFLICT(path) DO UPDATE SET
 			source_path = excluded.source_path,
 			mtime = excluded.mtime,
+			mtime_nsec = excluded.mtime_nsec,
 			size = excluded.size,
 			mode = excluded.mode,
 			uid = excluded.uid,
@@ -460,7 +468,7 @@ func (r *FileRepository) scanFileFrom(row fileRowScanner) (*File, error) {
 	var (
 		file                          File
 		idStr, pathStr, sourcePathStr string
-		mtimeUnix                     int64
+		mtimeUnix, mtimeNsec          int64
 		linkTarget                    sql.NullString
 	)
 
@@ -469,6 +477,7 @@ func (r *FileRepository) scanFileFrom(row fileRowScanner) (*File, error) {
 		&pathStr,
 		&sourcePathStr,
 		&mtimeUnix,
+		&mtimeNsec,
 		&file.Size,
 		&file.Mode,
 		&file.UID,
@@ -487,7 +496,7 @@ func (r *FileRepository) scanFileFrom(row fileRowScanner) (*File, error) {
 	file.Path = types.FilePath(pathStr)
 	file.SourcePath = types.SourcePath(sourcePathStr)
 
-	file.MTime = time.Unix(mtimeUnix, 0).UTC()
+	file.MTime = time.Unix(mtimeUnix, mtimeNsec).UTC()
 	if linkTarget.Valid {
 		file.LinkTarget = types.FilePath(linkTarget.String)
 	}

internal/database/files_test.go

@@ -252,6 +252,115 @@ func TestFileRepositorySymlink(t *testing.T) {
 	}
 }
 
+// An mtime after 2262 or before 1678 does not fit in int64 nanoseconds
+// since the epoch, and must still come back from the database unchanged.
+func TestFileRepositoryMTimeOutsideInt64NanosecondRange(t *testing.T) {
+	t.Parallel()
+
+	db, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+	repo := database.NewFileRepository(db)
+
+	mtimes := []time.Time{
+		time.Date(2300, time.January, 1, 0, 0, 0, 123456789, time.UTC),
+		time.Date(1601, time.January, 1, 0, 0, 0, 987654321, time.UTC),
+	}
+
+	for _, mtime := range mtimes {
+		created := &database.File{
+			Path:  types.FilePath("/created-" + mtime.Format(time.RFC3339Nano)),
+			MTime: mtime,
+		}
+
+		err := repo.Create(ctx, nil, created)
+		if err != nil {
+			t.Fatalf("failed to create file: %v", err)
+		}
+
+		batched := &database.File{
+			ID:    types.NewFileID(),
+			Path:  types.FilePath("/batched-" + mtime.Format(time.RFC3339Nano)),
+			MTime: mtime,
+		}
+
+		err = repo.CreateBatch(ctx, nil, []*database.File{batched})
+		if err != nil {
+			t.Fatalf("failed to batch create file: %v", err)
+		}
+
+		for _, path := range []types.FilePath{created.Path, batched.Path} {
+			retrieved, err := repo.GetByPath(ctx, path.String())
+			if err != nil {
+				t.Fatalf("failed to get file: %v", err)
+			}
+
+			if !retrieved.MTime.Equal(mtime) {
+				t.Errorf("%s: mtime got %v, want %v",
+					path, retrieved.MTime, mtime)
+			}
+		}
+	}
+}
+
+// A file already in the index and rewritten within the same second must get
+// its new nanoseconds stored, through both Create and CreateBatch.
+func TestFileRepositoryUpsertMTimeInSameSecond(t *testing.T) {
+	t.Parallel()
+
+	db, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+	repo := database.NewFileRepository(db)
+
+	indexed := time.Date(2026, time.October, 7, 12, 0, 0, 100000000, time.UTC)
+	rewritten := indexed.Add(800 * time.Millisecond)
+
+	tests := []struct {
+		name   string
+		upsert func(file *database.File) error
+	}{
+		{"Create", func(file *database.File) error {
+			return repo.Create(ctx, nil, file)
+		}},
+		{"CreateBatch", func(file *database.File) error {
+			return repo.CreateBatch(ctx, nil, []*database.File{file})
+		}},
+	}
+
+	for _, tt := range tests {
+		file := &database.File{
+			ID:    types.NewFileID(),
+			Path:  types.FilePath("/" + tt.name),
+			MTime: indexed,
+		}
+
+		err := tt.upsert(file)
+		if err != nil {
+			t.Fatalf("%s: failed to create file: %v", tt.name, err)
+		}
+
+		file.MTime = rewritten
+
+		err = tt.upsert(file)
+		if err != nil {
+			t.Fatalf("%s: failed to update file: %v", tt.name, err)
+		}
+
+		retrieved, err := repo.GetByPath(ctx, file.Path.String())
+		if err != nil {
+			t.Fatalf("%s: failed to get file: %v", tt.name, err)
+		}
+
+		if !retrieved.MTime.Equal(rewritten) {
+			t.Errorf("%s: mtime got %v, want %v",
+				tt.name, retrieved.MTime, rewritten)
+		}
+	}
+}
+
 func TestFileRepositoryTransaction(t *testing.T) {
 	t.Parallel()
 

internal/database/repository_edge_cases_test.go

@@ -606,8 +606,7 @@ func TestTimezoneHandling(t *testing.T) {
 		t.Skip("timezone not available")
 	}
 
-	// Use Truncate to remove sub-second precision since we store as Unix timestamps
-	nyTime := time.Now().In(loc).Truncate(time.Second)
+	nyTime := time.Now().In(loc)
 	file := &File{
 		Path:  "/timezone-test.txt",
 		MTime: nyTime,

internal/database/schema/001.sql

@@ -6,7 +6,8 @@ CREATE TABLE IF NOT EXISTS files (
     id TEXT PRIMARY KEY,  -- UUID
     path TEXT NOT NULL UNIQUE,
     source_path TEXT NOT NULL DEFAULT '',  -- The source directory this file came from (for restore path stripping)
-    mtime INTEGER NOT NULL,
+    mtime INTEGER NOT NULL,  -- whole seconds since the Unix epoch
+    mtime_nsec INTEGER NOT NULL,  -- nanoseconds within that second, 0 to 999999999
     size INTEGER NOT NULL,
     mode INTEGER NOT NULL,
     uid INTEGER NOT NULL,

internal/snapshot/scanner.go

@@ -1221,7 +1221,7 @@ func (s *Scanner) checkFileInMemory(
 
 	// Check if file has changed
 	if existingFile.Size != file.Size ||
-		existingFile.MTime.Unix() != file.MTime.Unix() ||
+		!existingFile.MTime.Equal(file.MTime) ||
 		existingFile.Mode != file.Mode ||
 		existingFile.UID != file.UID ||
 		existingFile.GID != file.GID {

internal/vaultik/info.go

@@ -207,13 +207,18 @@ type RemoteInfoResult struct {
 	ReferencedBlobSize  int64 `json:"referenced_blob_size"`
 
 	// Orphaned blobs. Both stay nil (null in the JSON) when a manifest
-	// could not be read, since that snapshot's blobs would be counted
-	// as orphaned.
+	// could not be read or a name under metadata/ was skipped, since
+	// that snapshot's blobs would be counted as orphaned.
 	OrphanedBlobCount *int   `json:"orphaned_blob_count"`
 	OrphanedBlobSize  *int64 `json:"orphaned_blob_size"`
 
 	// Remote key of each snapshot whose manifest could not be read
 	UnreadableManifests []string `json:"unreadable_manifests,omitempty"`
+
+	// Number of names under metadata/ skipped because they are not
+	// remote keys. The names themselves are not reported: they come
+	// from the destination store and may hold control characters.
+	SkippedMetadataNames int `json:"skipped_metadata_names,omitempty"`
 }
 
 // RemoteInfo displays information about remote storage
@@ -239,11 +244,13 @@ func (v *Vaultik) RemoteInfo(jsonOutput bool) error {
 		v.stdoutf("Scanning snapshot metadata...\n")
 	}
 
-	snapshotMetadata, snapshotIDs, err := v.collectSnapshotMetadata()
+	snapshotMetadata, snapshotIDs, skippedNames, err := v.collectSnapshotMetadata()
 	if err != nil {
 		return err
 	}
 
+	result.SkippedMetadataNames = skippedNames
+
 	if showText {
 		v.stdoutf("Downloading %d manifest(s)...\n", len(snapshotIDs))
 	}
@@ -280,16 +287,18 @@ func (v *Vaultik) RemoteInfo(jsonOutput bool) error {
 }
 
 // collectSnapshotMetadata scans remote metadata and returns
-// per-snapshot info and sorted IDs.
+// per-snapshot info, sorted IDs and the number of names it skipped
+// because they are not remote keys.
 func (v *Vaultik) collectSnapshotMetadata() (
-	map[string]*SnapshotMetadataInfo, []string, error,
+	map[string]*SnapshotMetadataInfo, []string, int, error,
 ) {
 	snapshotMetadata := make(map[string]*SnapshotMetadataInfo)
+	skippedNames := make(map[string]bool)
 
 	metadataCh := v.Storage.ListStream(v.ctx, "metadata/")
 	for obj := range metadataCh {
 		if obj.Err != nil {
-			return nil, nil, fmt.Errorf("listing metadata: %w", obj.Err)
+			return nil, nil, 0, fmt.Errorf("listing metadata: %w", obj.Err)
 		}
 
 		parts := strings.Split(obj.Key, "/")
@@ -306,6 +315,8 @@ func (v *Vaultik) collectSnapshotMetadata() (
 			log.Warn("Skipping non-conforming key under metadata/",
 				"key", obj.Key)
 
+			skippedNames[snapshotID] = true
+
 			continue
 		}
 
@@ -332,7 +343,7 @@ func (v *Vaultik) collectSnapshotMetadata() (
 
 	sort.Strings(snapshotIDs)
 
-	return snapshotMetadata, snapshotIDs, nil
+	return snapshotMetadata, snapshotIDs, len(skippedNames), nil
 }
 
 // collectReferencedBlobsFromManifests downloads manifests and returns
@@ -400,9 +411,9 @@ func (v *Vaultik) populateRemoteInfoResult(
 }
 
 // scanRemoteBlobStorage lists all blobs on remote and computes orphan
-// stats when every manifest was read. showText is true only when the
-// human report is being printed (not --json, not --quiet), gating the
-// progress line.
+// stats when every manifest was read and no name under metadata/ was
+// skipped. showText is true only when the human report is being
+// printed (not --json, not --quiet), gating the progress line.
 func (v *Vaultik) scanRemoteBlobStorage(
 	result *RemoteInfoResult, referencedBlobs map[string]int64, showText bool,
 ) error {
@@ -429,9 +440,10 @@ func (v *Vaultik) scanRemoteBlobStorage(
 		result.TotalBlobSize += obj.Size
 	}
 
-	// A blob named only by a manifest that could not be read would be
-	// counted as orphaned, so the orphan figures stay unknown.
-	if len(result.UnreadableManifests) > 0 {
+	// A blob named only by a manifest that could not be read, or by one
+	// under a skipped name, would be counted as orphaned, so the orphan
+	// figures stay unknown.
+	if len(result.UnreadableManifests) > 0 || result.SkippedMetadataNames > 0 {
 		return nil
 	}
 
@@ -505,8 +517,9 @@ func (v *Vaultik) printRemoteInfoTable(result *RemoteInfoResult) {
 
 	if result.OrphanedBlobCount == nil {
 		v.stdoutf("Orphaned (unreferenced):    unknown "+
-			"(%d manifest(s) could not be read)\n",
-			len(result.UnreadableManifests))
+			"(%d manifest(s) could not be read, "+
+			"%d name(s) under metadata/ skipped)\n",
+			len(result.UnreadableManifests), result.SkippedMetadataNames)
 
 		return
 	}

internal/vaultik/remote_info_test.go

@@ -13,6 +13,11 @@ import (
 	"sneak.berlin/go/vaultik/internal/snapshot"
 )
 
+// testBlobHashB is a blob that the manifest written by addRemote does
+// not reference.
+const testBlobHashB = "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb" +
+	"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"
+
 // TestRemoteInfo_UnreadableManifestLeavesOrphansUnknown checks that a
 // manifest remote info cannot read makes the orphan figures unknown. A
 // blob referenced only by that snapshot would otherwise be counted as
@@ -21,9 +26,6 @@ func TestRemoteInfo_UnreadableManifestLeavesOrphansUnknown(t *testing.T) {
 	log.Initialize(log.Config{})
 	t.Parallel()
 
-	const testBlobHashB = "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb" +
-		"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"
-
 	env := newListEnv(t)
 
 	// The readable manifest references blob A only.
@@ -50,8 +52,8 @@ func TestRemoteInfo_UnreadableManifestLeavesOrphansUnknown(t *testing.T) {
 	require.NoError(t, env.v.RemoteInfo(false))
 
 	text := env.stdout.String()
-	assert.Contains(t, text,
-		"Orphaned (unreferenced):    unknown (1 manifest(s) could not be read)")
+	assert.Contains(t, text, "Orphaned (unreferenced):    unknown "+
+		"(1 manifest(s) could not be read, 0 name(s) under metadata/ skipped)")
 	assert.NotContains(t, text, "vaultik prune")
 
 	env.stdout.Reset()
@@ -68,21 +70,45 @@ func TestRemoteInfo_UnreadableManifestLeavesOrphansUnknown(t *testing.T) {
 
 // TestRemoteInfo_SkipsNonConformingMetadataName checks that a directory
 // under metadata/ whose name is not a remote key is left out of the
-// report. The name comes from the destination store; printed raw, its
-// control characters would reach the terminal.
+// report, and that the orphan figures are then unknown. The name comes
+// from the destination store; printed raw, its control characters would
+// reach the terminal. Its manifest is not read, so a blob only it
+// references would otherwise be counted as orphaned.
 func TestRemoteInfo_SkipsNonConformingMetadataName(t *testing.T) {
 	log.Initialize(log.Config{})
 	t.Parallel()
 
 	env := newListEnv(t)
 	env.addRemote(t, listRemoteID, time.Date(2026, 3, 2, 0, 0, 0, 0, time.UTC))
+	addBlob(t, env.store.testStorer, testBlobHashA)
+	addBlob(t, env.store.testStorer, testBlobHashB)
 	require.NoError(t, env.store.Put(context.Background(),
 		"metadata/\x1b[31mred/manifest.json.zst",
 		bytes.NewReader([]byte("not a valid manifest"))))
 
 	require.NoError(t, env.v.RemoteInfo(false))
 
+	text := env.stdout.String()
+	assert.NotContains(t, text, "\x1b")
+	assert.NotContains(t, text, "31mred")
+	assert.Contains(t, text, "Total (1 snapshots)")
+	assert.Contains(t, text, "Orphaned (unreferenced):    unknown "+
+		"(0 manifest(s) could not be read, 1 name(s) under metadata/ skipped)")
+	assert.NotContains(t, text, "vaultik prune")
+
+	env.stdout.Reset()
+	require.NoError(t, env.v.RemoteInfo(true))
+
 	out := env.stdout.String()
-	assert.NotContains(t, out, "\x1b")
-	assert.Contains(t, out, "Total (1 snapshots)")
+	assert.NotContains(t, out, "31mred")
+
+	var doc map[string]any
+
+	require.NoError(t, json.Unmarshal([]byte(out), &doc))
+	assert.Contains(t, doc, "orphaned_blob_count")
+	assert.Nil(t, doc["orphaned_blob_count"])
+	assert.Contains(t, doc, "orphaned_blob_size")
+	assert.Nil(t, doc["orphaned_blob_size"])
+	assert.InDelta(t, 1, doc["skipped_metadata_names"], 0)
+	assert.NotContains(t, doc, "unreadable_manifests")
 }

internal/vaultik/same_second_rewrite_test.go

@@ -0,0 +1,73 @@
+package vaultik_test
+
+import (
+	"bytes"
+	"context"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/require"
+	"sneak.berlin/go/vaultik/internal/database"
+	"sneak.berlin/go/vaultik/internal/log"
+	"sneak.berlin/go/vaultik/internal/storage"
+	"sneak.berlin/go/vaultik/internal/vaultik"
+)
+
+// A file rewritten with its size unchanged and a new mtime in the same
+// second as the mtime the index holds must still be backed up. See
+// https://git.eeqj.de/sneak/vaultik/issues/226.
+//
+//nolint:paralleltest // installs the global logger via log.Initialize
+func TestBackupOfSameSecondRewriteRestoresNewContent(t *testing.T) {
+	log.Initialize(log.Config{})
+
+	fs := afero.NewOsFs()
+	tempDir := t.TempDir()
+	dataDir := filepath.Join(tempDir, "src")
+	storeDir := filepath.Join(tempDir, "remote")
+	restoreDir := filepath.Join(tempDir, "restored")
+	dbPath := filepath.Join(tempDir, "index.sqlite")
+	rewrittenPath := filepath.Join(dataDir, "small.txt")
+
+	ctx := context.Background()
+	files := writeFaultSourceTree(t, fs, dataDir)
+	cfg := changedFileConfig(dataDir, dbPath)
+
+	firstMTime := time.Date(2026, time.January, 2, 3, 4, 5, 0, time.UTC).
+		Add(100 * time.Millisecond)
+	secondMTime := firstMTime.Add(800 * time.Millisecond)
+
+	require.NoError(t, fs.Chtimes(rewrittenPath, firstMTime, firstMTime))
+
+	store, err := storage.NewFileStorer(storeDir)
+	require.NoError(t, err)
+
+	db, err := database.New(ctx, dbPath)
+	require.NoError(t, err)
+
+	repos := database.NewRepositories(db)
+	v := newBackupVaultik(ctx, cfg, store, repos, db, fs)
+
+	require.NoError(t, backUp(v, "first"))
+
+	// Upper-casing ASCII text keeps its size.
+	files[rewrittenPath] = bytes.ToUpper(files[rewrittenPath])
+	require.NoError(t, afero.WriteFile(fs, rewrittenPath, files[rewrittenPath], 0o644))
+	require.NoError(t, fs.Chtimes(rewrittenPath, secondMTime, secondMTime))
+
+	require.NoError(t, backUp(v, "second"))
+
+	id := localSnapshotID(ctx, t, repos, "second")
+	require.NoError(t, db.Close())
+
+	reader := newReaderVaultik(ctx, cfg, store, nil, fs)
+	require.NoError(t, reader.Restore(&vaultik.RestoreOptions{
+		SnapshotID: id,
+		TargetDir:  restoreDir,
+		Verify:     true,
+	}))
+
+	assertRestoredTree(t, fs, restoreDir, files)
+}