Store and compare file mtimes in nanoseconds (closes #226)

The files table held mtime in whole seconds and the scanner compared
whole seconds. A file rewritten with its size unchanged and a new mtime
in the same second as the indexed one was treated as unchanged, and
every later snapshot restored the old content. mtime is now stored as
nanoseconds since the Unix epoch and compared at that precision.

A local index written before this change holds seconds in mtime: its
next backup re-chunks every file once, and a restore of a snapshot made
before it sets mtimes near 1970.

An mtime outside the years 1678 to 2262 does not fit in int64
nanoseconds; it is stored wrong and restored wrong.

Model: opus-5-5

TODO.md

@@ -22,6 +22,16 @@ the tag exists and is exercised; what is left is merging `next` to
 
 # Completed Steps
 
+- 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. `mtime`
+  now holds nanoseconds since the Unix epoch and is compared at that
+  precision. A local index written before the change holds seconds
+  there, so its next backup re-chunks every file once; chunks it already
+  stored are not uploaded again.
+
 - 2026-10-06: Made the backup summary and the `snapshots` row count each
   file, byte and upload once
   ([issue #225](https://git.eeqj.de/sneak/vaultik/issues/225)). The

docs/DATAMODEL.md

@@ -36,7 +36,7 @@ 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 in nanoseconds since the Unix epoch
 - `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

@@ -54,16 +54,16 @@ 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.UnixNano(), 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.UnixNano(), 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.UnixNano(), file.Size, file.Mode, file.UID, file.GID,
 			file.LinkTarget.String()).Scan(&idStr)
 	}
 
@@ -164,7 +164,7 @@ func (r *FileRepository) ListModifiedSince(
 		ORDER BY path
 	`
 
-	rows, err := r.db.conn.QueryContext(ctx, query, since.Unix())
+	rows, err := r.db.conn.QueryContext(ctx, query, since.UnixNano())
 	if err != nil {
 		return nil, fmt.Errorf("querying files: %w", err)
 	}
@@ -392,7 +392,7 @@ func (r *FileRepository) CreateBatch(
 
 			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.UnixNano(), f.Size, f.Mode, f.UID, f.GID,
 				f.LinkTarget.String())
 		}
 
@@ -460,7 +460,7 @@ func (r *FileRepository) scanFileFrom(row fileRowScanner) (*File, error) {
 	var (
 		file                          File
 		idStr, pathStr, sourcePathStr string
-		mtimeUnix                     int64
+		mtimeUnixNano                 int64
 		linkTarget                    sql.NullString
 	)
 
@@ -468,7 +468,7 @@ func (r *FileRepository) scanFileFrom(row fileRowScanner) (*File, error) {
 		&idStr,
 		&pathStr,
 		&sourcePathStr,
-		&mtimeUnix,
+		&mtimeUnixNano,
 		&file.Size,
 		&file.Mode,
 		&file.UID,
@@ -487,7 +487,7 @@ 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(0, mtimeUnixNano).UTC()
 	if linkTarget.Valid {
 		file.LinkTarget = types.FilePath(linkTarget.String)
 	}

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 +6,7 @@ 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,  -- nanoseconds since the Unix epoch
     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.UnixNano() != file.MTime.UnixNano() ||
 		existingFile.Mode != file.Mode ||
 		existingFile.UID != file.UID ||
 		existingFile.GID != file.GID {

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)
+}