Back up symlinks, empty directories, and file permissions

Scanner now records symlinks (with their target) and directories
during the walk phase instead of skipping them. processFileStreaming
detects non-regular entries and writes the DB record without chunking.

The e2e test (TestEndToEndFileStorage) now verifies:
- Symlink target preserved through backup→restore
- Empty directory survives round-trip
- File permissions (0600) restored correctly

internal/snapshot/scanner.go

@@ -649,7 +649,40 @@ func (s *Scanner) scanPhase(ctx context.Context, path string, result *ScanResult
 			return nil
 		}
 
-		// Skip non-regular files for processing (but still count them)
+		// Handle symlinks
+		if info.Mode()&os.ModeSymlink != 0 {
+			file := s.buildSymlinkEntry(filePath, info)
+			if file != nil {
+				existingFiles[filePath] = struct{}{}
+				mu.Lock()
+				filesToProcess = append(filesToProcess, &FileToProcess{
+					Path:     filePath,
+					FileInfo: info,
+					File:     file,
+				})
+				filesScanned++
+				mu.Unlock()
+				s.updateScanEntryStats(result, true, info)
+			}
+			return nil
+		}
+
+		// Handle directories (record for permission/ownership preservation and empty-dir support)
+		if info.IsDir() {
+			file := s.buildDirectoryEntry(filePath, info)
+			existingFiles[filePath] = struct{}{}
+			mu.Lock()
+			filesToProcess = append(filesToProcess, &FileToProcess{
+				Path:     filePath,
+				FileInfo: info,
+				File:     file,
+			})
+			filesScanned++
+			mu.Unlock()
+			return nil
+		}
+
+		// Skip other non-regular files (devices, sockets, etc.)
 		if !info.Mode().IsRegular() {
 			return nil
 		}
@@ -760,6 +793,71 @@ func (s *Scanner) printScanProgressLine(filesScanned int64, changedCount int, es
 	}
 }
 
+// buildSymlinkEntry creates a File record for a symlink.
+// Returns nil if the link target cannot be read.
+func (s *Scanner) buildSymlinkEntry(path string, info os.FileInfo) *database.File {
+	target, err := os.Readlink(path)
+	if err != nil {
+		log.Debug("Cannot read symlink target", "path", path, "error", err)
+		return nil
+	}
+
+	var uid, gid uint32
+	if stat, ok := info.Sys().(interface {
+		Uid() uint32
+		Gid() uint32
+	}); ok {
+		uid = stat.Uid()
+		gid = stat.Gid()
+	}
+
+	return &database.File{
+		ID:         types.NewFileID(),
+		Path:       types.FilePath(path),
+		SourcePath: types.SourcePath(s.currentSourcePath),
+		MTime:      info.ModTime(),
+		Size:       0,
+		Mode:       uint32(info.Mode()),
+		UID:        uid,
+		GID:        gid,
+		LinkTarget: types.FilePath(target),
+	}
+}
+
+// buildDirectoryEntry creates a File record for a directory.
+func (s *Scanner) buildDirectoryEntry(path string, info os.FileInfo) *database.File {
+	var uid, gid uint32
+	if stat, ok := info.Sys().(interface {
+		Uid() uint32
+		Gid() uint32
+	}); ok {
+		uid = stat.Uid()
+		gid = stat.Gid()
+	}
+
+	return &database.File{
+		ID:         types.NewFileID(),
+		Path:       types.FilePath(path),
+		SourcePath: types.SourcePath(s.currentSourcePath),
+		MTime:      info.ModTime(),
+		Size:       0,
+		Mode:       uint32(info.Mode()),
+		UID:        uid,
+		GID:        gid,
+	}
+}
+
+// recordNonRegularFile writes a symlink or directory entry to the database
+// and associates it with the current snapshot. No chunking is performed.
+func (s *Scanner) recordNonRegularFile(ctx context.Context, ftp *FileToProcess) error {
+	return s.repos.WithTx(ctx, func(txCtx context.Context, tx *sql.Tx) error {
+		if err := s.repos.Files.Create(txCtx, tx, ftp.File); err != nil {
+			return fmt.Errorf("creating non-regular file record: %w", err)
+		}
+		return s.repos.Snapshots.AddFileByID(txCtx, tx, s.snapshotID, ftp.File.ID)
+	})
+}
+
 // checkFileInMemory checks if a file needs processing using the in-memory map
 // No database access is performed - this is purely CPU/memory work
 func (s *Scanner) checkFileInMemory(path string, info os.FileInfo, knownFiles map[string]*database.File) (*database.File, bool) {
@@ -1184,6 +1282,12 @@ type streamingChunkInfo struct {
 
 // processFileStreaming processes a file by streaming chunks directly to the packer
 func (s *Scanner) processFileStreaming(ctx context.Context, fileToProcess *FileToProcess, result *ScanResult) error {
+	// Symlinks and directories have no data to chunk — just record them in the DB.
+	mode := os.FileMode(fileToProcess.File.Mode)
+	if mode&os.ModeSymlink != 0 || mode.IsDir() {
+		return s.recordNonRegularFile(ctx, fileToProcess)
+	}
+
 	file, err := s.fs.Open(fileToProcess.Path)
 	if err != nil {
 		return fmt.Errorf("opening file: %w", err)

internal/snapshot/scanner_test.go

@@ -110,15 +110,15 @@ func TestScannerSimpleDirectory(t *testing.T) {
 		t.Errorf("expected at least 97 bytes scanned, got %d", result.BytesScanned)
 	}
 
-	// Verify files in database - only regular files are stored
+	// Verify files in database - includes regular files and directories
 	files, err := repos.Files.ListByPrefix(ctx, "/source")
 	if err != nil {
 		t.Fatalf("failed to list files: %v", err)
 	}
 
-	// We should have 6 files (directories are not stored)
-	if len(files) != 6 {
-		t.Errorf("expected 6 files in database, got %d", len(files))
+	// 6 regular files + 3 directories (/source, /source/subdir, /source/subdir2)
+	if len(files) != 9 {
+		t.Errorf("expected 9 entries in database (6 files + 3 dirs), got %d", len(files))
 	}
 
 	// Verify specific file

internal/vaultik/integration_test.go

@@ -585,6 +585,19 @@ func TestEndToEndFileStorage(t *testing.T) {
 		require.NoError(t, afero.WriteFile(fs, path, content, 0o644))
 	}
 
+	// Create a file with non-default permissions.
+	restrictedPath := filepath.Join(dataDir, "restricted.txt")
+	require.NoError(t, afero.WriteFile(fs, restrictedPath, []byte("secret"), 0o600))
+	testFiles[restrictedPath] = []byte("secret")
+
+	// Create an empty directory (should survive round-trip).
+	emptyDir := filepath.Join(dataDir, "emptydir")
+	require.NoError(t, fs.MkdirAll(emptyDir, 0o755))
+
+	// Create a symlink.
+	symlinkPath := filepath.Join(dataDir, "link-to-small")
+	require.NoError(t, os.Symlink("small.txt", symlinkPath))
+
 	// FileStorer is the real-world local-disk backend.
 	storer, err := storage.NewFileStorer(storeDir)
 	require.NoError(t, err)
@@ -669,6 +682,25 @@ func TestEndToEndFileStorage(t *testing.T) {
 		require.NoError(t, err, "restored file missing: %s", restoredPath)
 		require.Equalf(t, expected, got, "byte-equality failed for %s", origPath)
 	}
+
+	// Verify the restricted file kept its permissions.
+	restoredRestricted := filepath.Join(restoreDir, restrictedPath)
+	rInfo, err := os.Stat(restoredRestricted)
+	require.NoError(t, err)
+	assert.Equal(t, os.FileMode(0o600), rInfo.Mode().Perm(),
+		"restricted file should preserve 0600 permissions")
+
+	// Verify the empty directory was restored.
+	restoredEmptyDir := filepath.Join(restoreDir, emptyDir)
+	dInfo, err := os.Stat(restoredEmptyDir)
+	require.NoError(t, err, "empty directory should be restored")
+	assert.True(t, dInfo.IsDir(), "emptydir should be a directory")
+
+	// Verify the symlink was restored with the correct target.
+	restoredSymlink := filepath.Join(restoreDir, symlinkPath)
+	target, err := os.Readlink(restoredSymlink)
+	require.NoError(t, err, "symlink should be restored")
+	assert.Equal(t, "small.txt", target, "symlink target should be preserved")
 }
 
 // bytesPattern returns a deterministic byte slice of length n with a tag prefix,