Count a file as deleted only if the previous snapshot of its name had it (closes #304)

A backup counted as deleted every file in the local index under the
source path that the walk did not find. That took in files the
snapshot excludes but another snapshot backs up, and files removed long
ago, which every later backup, and the first backup of another name
over the same path, reported as deleted again.

The backup now looks up the most recent completed snapshot of the same
name and counts only the files it lists that the walk did not find. A
file that is excluded, or inside an excluded directory, is not counted.

The snapshots row stores no deleted figure; only the backup's output
changes.

Model: opus-5-5

ARCHITECTURE.md

@@ -279,8 +279,8 @@ Key methods:
 - `Scan(ctx, path, snapshotID)` → Main scan operation
 
 Scan phases:
-1. **Phase 0**: Detect deleted files from previous snapshots
-2. **Phase 1**: Walk directory, identify files needing processing
+1. **Phase 1**: Walk directory, identify files needing processing
+2. **Phase 1b**: Count as deleted the files that the previous snapshot of the same name lists and the walk did not find; a file that is excluded, or inside an excluded directory, is not counted
 3. **Phase 2**: Process files (chunk → pack → upload)
 
 #### SnapshotManager
@@ -320,13 +320,13 @@ CreateSnapshot(opts)
     │       │
     │       ├─► scanner.Scan(ctx, path, snapshotID)
     │       │       │
-    │       │       ├─► Phase 0: detectDeletedFiles()
-    │       │       │
     │       │       ├─► Phase 1: scanPhase()
     │       │       │       Walk directory
     │       │       │       Check file metadata changes
     │       │       │       Build list of files to process
     │       │       │
+    │       │       ├─► Phase 1b: detectDeletedFiles()
+    │       │       │
     │       │       └─► Phase 2: processPhase()
     │       │               For each file:
     │       │                   chunker.ChunkReaderStreaming()

internal/database/files.go

@@ -277,6 +277,50 @@ func (r *FileRepository) ListUnderPath(
 	return files, rows.Err()
 }
 
+// ListUnderPathInSnapshot returns the files that ListUnderPath returns
+// for path and that the snapshot lists, in no particular order.
+func (r *FileRepository) ListUnderPathInSnapshot(
+	ctx context.Context, path, snapshotID string,
+) ([]*File, error) {
+	path = strings.TrimRight(path, "/")
+	dirPrefix := path + "/"
+
+	query := `
+		SELECT f.id, f.path, f.source_path, f.mtime, f.mtime_nsec, f.size,
+			f.mode, f.uid, f.gid, f.link_target
+		FROM files f
+		JOIN snapshot_files sf ON sf.file_id = f.id
+		WHERE sf.snapshot_id = ?
+		  AND (f.path = ? OR substr(f.path, 1, length(?)) = ?)
+	`
+
+	rows, err := r.db.conn.QueryContext(ctx, query,
+		snapshotID, path, dirPrefix, dirPrefix)
+	if err != nil {
+		return nil, fmt.Errorf("querying files: %w", err)
+	}
+
+	defer func() {
+		err := rows.Close()
+		if err != nil {
+			Fatalf("failed to close rows: %v", err)
+		}
+	}()
+
+	var files []*File
+
+	for rows.Next() {
+		file, err := r.scanFileRows(rows)
+		if err != nil {
+			return nil, fmt.Errorf("scanning file: %w", err)
+		}
+
+		files = append(files, file)
+	}
+
+	return files, rows.Err()
+}
+
 // ListIDsWithChunksNotInUploadedBlobs returns the IDs of the files whose
 // path starts with prefix and that list at least one chunk held by no
 // blob whose upload has completed (uploaded_ts set). A new snapshot

internal/database/files_test.go

@@ -212,6 +212,65 @@ func TestFileRepositoryListUnderPath(t *testing.T) {
 	}
 }
 
+// ListUnderPathInSnapshot leaves out files outside path and files the
+// snapshot does not list, though another snapshot lists them.
+func TestFileRepositoryListUnderPathInSnapshot(t *testing.T) {
+	t.Parallel()
+
+	db, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+	files := database.NewFileRepository(db)
+	snapshots := database.NewSnapshotRepository(db)
+
+	listed := map[string][]string{
+		"one": {"/src/a.txt", "/src2/c.txt"},
+		"two": {"/src/b.txt"},
+	}
+
+	for snapshotID, paths := range listed {
+		err := snapshots.Create(ctx, nil, &database.Snapshot{
+			ID:        types.SnapshotID(snapshotID),
+			Hostname:  "host",
+			StartedAt: time.Now(),
+		})
+		if err != nil {
+			t.Fatalf("failed to create snapshot %s: %v", snapshotID, err)
+		}
+
+		for _, path := range paths {
+			err := files.Create(ctx, nil, &database.File{
+				Path:  types.FilePath(path),
+				MTime: time.Now().Truncate(time.Second),
+				Mode:  0644,
+			})
+			if err != nil {
+				t.Fatalf("failed to create %s: %v", path, err)
+			}
+
+			err = snapshots.AddFile(ctx, nil, snapshotID, path)
+			if err != nil {
+				t.Fatalf("failed to add %s to %s: %v", path, snapshotID, err)
+			}
+		}
+	}
+
+	found, err := files.ListUnderPathInSnapshot(ctx, "/src", "one")
+	if err != nil {
+		t.Fatalf("failed to list files: %v", err)
+	}
+
+	got := make([]string, 0, len(found))
+	for _, f := range found {
+		got = append(got, f.Path.String())
+	}
+
+	if !slices.Equal(got, []string{"/src/a.txt"}) {
+		t.Errorf("got %q, want only /src/a.txt", got)
+	}
+}
+
 func TestFileRepositorySymlink(t *testing.T) {
 	t.Parallel()
 

internal/snapshot/module.go

@@ -16,6 +16,9 @@ type ScannerParams struct {
 	Fs             afero.Fs
 	Exclude        []string // Exclude patterns (combined global + snapshot-specific)
 	SkipErrors     bool     // Skip file read errors (log loudly but continue)
+	// PreviousSnapshotID is the most recent completed snapshot of the
+	// same name, "" for none.
+	PreviousSnapshotID string
 }
 
 // Module exports backup functionality as an fx module.
@@ -44,17 +47,18 @@ func provideScannerFactory(
 		}
 
 		return NewScanner(ScannerConfig{
-			FS:               params.Fs,
-			ChunkSize:        cfg.ChunkSize.Int64(),
-			Repositories:     repos,
-			Storage:          storer,
-			MaxBlobSize:      cfg.BlobSizeLimit.Int64(),
-			CompressionLevel: cfg.CompressionLevel,
-			AgeRecipients:    cfg.AgeRecipients,
-			EnableProgress:   params.EnableProgress,
-			UI:               params.UI,
-			Exclude:          excludes,
-			SkipErrors:       params.SkipErrors,
+			FS:                 params.Fs,
+			ChunkSize:          cfg.ChunkSize.Int64(),
+			Repositories:       repos,
+			Storage:            storer,
+			MaxBlobSize:        cfg.BlobSizeLimit.Int64(),
+			CompressionLevel:   cfg.CompressionLevel,
+			AgeRecipients:      cfg.AgeRecipients,
+			EnableProgress:     params.EnableProgress,
+			UI:                 params.UI,
+			Exclude:            excludes,
+			SkipErrors:         params.SkipErrors,
+			PreviousSnapshotID: params.PreviousSnapshotID,
 		})
 	}
 }

internal/snapshot/scanner.go

@@ -58,6 +58,10 @@ type Scanner struct {
 	compressionLevel int
 	ageRecipient     string
 	snapshotID       string // Current snapshot being processed
+	// previousSnapshotID is the most recent completed snapshot of the
+	// same name, "" for none. Only a file it lists can be counted as
+	// deleted.
+	previousSnapshotID string
 	// currentSourcePath is the source directory being scanned, stored with
 	// each file record.
 	currentSourcePath string
@@ -129,6 +133,9 @@ type ScannerConfig struct {
 	// SkipErrors skips files that cannot be opened or read (log loudly but
 	// continue); packer, database, encryption, and upload errors still abort.
 	SkipErrors bool
+	// PreviousSnapshotID is the most recent completed snapshot of the
+	// same name, "" for none.
+	PreviousSnapshotID string
 }
 
 // ScanResult contains the results of a scan operation. Files and bytes
@@ -204,6 +211,7 @@ func NewScanner(cfg ScannerConfig) *Scanner {
 		compiledExclude:    compiledExclude,
 		progress:           progress,
 		skipErrors:         cfg.SkipErrors,
+		previousSnapshotID: cfg.PreviousSnapshotID,
 		ui:                 uiw,
 		pendingChunkHashes: make(map[string]struct{}),
 	}
@@ -255,8 +263,9 @@ func (s *Scanner) Scan(
 
 	filesToProcess := scanResult.FilesToProcess
 
-	// Phase 1b: Detect deleted files by comparing DB against scanned files
-	err = s.detectDeletedFilesFromMap(ctx, knownFiles, existingFiles, result)
+	// Phase 1b: Detect deleted files by comparing the previous snapshot
+	// of this name against scanned files
+	err = s.detectDeletedFiles(ctx, path, existingFiles, result)
 	if err != nil {
 		return nil, fmt.Errorf("detecting deleted files: %w", err)
 	}
@@ -436,9 +445,8 @@ func (s *Scanner) summarizeScanPhase(
 }
 
 // loadKnownFiles loads the known files at and beneath path from the
-// database into a map for fast lookup. Every loaded file the scan does
-// not find is counted as deleted. This avoids per-file database queries
-// during the scan phase.
+// database into a map for fast lookup. This avoids per-file database
+// queries during the scan phase.
 func (s *Scanner) loadKnownFiles(
 	ctx context.Context, path string,
 ) (map[string]*database.File, error) {
@@ -1938,21 +1946,28 @@ func (s *Scanner) queueFileForBatchInsert(
 	})
 }
 
-// detectDeletedFilesFromMap finds files that existed in previous snapshots
-// but no longer exist. Uses pre-loaded maps to avoid any filesystem or
-// database access.
-func (s *Scanner) detectDeletedFilesFromMap(
+// detectDeletedFiles counts as deleted each file at or beneath path that
+// the previous snapshot of this name lists and the walk did not find.
+// A file that is excluded, or inside an excluded directory, is not
+// counted: the walk skips it whether or not it is still on disk.
+func (s *Scanner) detectDeletedFiles(
 	ctx context.Context,
-	knownFiles map[string]*database.File,
+	path string,
 	existingFiles map[string]struct{},
 	result *ScanResult,
 ) error {
-	if len(knownFiles) == 0 {
+	if s.previousSnapshotID == "" {
 		return nil
 	}
 
-	// Check each known file against the enumerated set (no filesystem access needed)
-	for path, file := range knownFiles {
+	previousFiles, err := s.repos.Files.ListUnderPathInSnapshot(
+		ctx, path, s.previousSnapshotID)
+	if err != nil {
+		return fmt.Errorf("listing files of snapshot %s: %w",
+			s.previousSnapshotID, err)
+	}
+
+	for _, file := range previousFiles {
 		// Check context cancellation periodically
 		select {
 		case <-ctx.Done():
@@ -1960,13 +1975,16 @@ func (s *Scanner) detectDeletedFilesFromMap(
 		default:
 		}
 
-		// Check if the file exists in our enumerated set
-		if _, exists := existingFiles[path]; !exists {
-			// File has been deleted
-			result.FilesDeleted++
-			result.BytesDeleted += file.Size
-			log.Debug("Detected deleted file", "path", path, "size", file.Size)
+		filePath := file.Path.String()
+
+		_, exists := existingFiles[filePath]
+		if exists || s.excludedOrInExcludedDir(filePath, path) {
+			continue
 		}
+
+		result.FilesDeleted++
+		result.BytesDeleted += file.Size
+		log.Debug("Detected deleted file", "path", filePath, "size", file.Size)
 	}
 
 	if result.FilesDeleted > 0 {
@@ -1977,6 +1995,20 @@ func (s *Scanner) detectDeletedFilesFromMap(
 	return nil
 }
 
+// excludedOrInExcludedDir reports whether filePath, which is at or
+// beneath rootPath, or any directory between rootPath and it, matches an
+// exclude pattern. A pattern such as **/node_modules matches the
+// directory but not the files inside it, which the walk skips too.
+func (s *Scanner) excludedOrInExcludedDir(filePath, rootPath string) bool {
+	for p := filePath; len(p) > len(rootPath); p = filepath.Dir(p) {
+		if s.shouldExclude(p, rootPath) {
+			return true
+		}
+	}
+
+	return false
+}
+
 // wrapPermissionError augments permission errors with platform-specific
 // remediation instructions. On macOS, TCC-protected directories (Calendars,
 // Reminders, Photos, etc.) return EPERM unless the running application has

internal/vaultik/fault_injection_test.go

@@ -661,17 +661,18 @@ func faultScannerFactory(
 ) snapshot.ScannerFactory {
 	return func(params snapshot.ScannerParams) *snapshot.Scanner {
 		return snapshot.NewScanner(snapshot.ScannerConfig{
-			FS:               params.Fs,
-			Storage:          storer,
-			ChunkSize:        faultChunkSize,
-			MaxBlobSize:      faultMaxBlobSize,
-			CompressionLevel: cfg.CompressionLevel,
-			AgeRecipients:    cfg.AgeRecipients,
-			Repositories:     repos,
-			EnableProgress:   params.EnableProgress,
-			UI:               params.UI,
-			Exclude:          params.Exclude,
-			SkipErrors:       params.SkipErrors,
+			FS:                 params.Fs,
+			Storage:            storer,
+			ChunkSize:          faultChunkSize,
+			MaxBlobSize:        faultMaxBlobSize,
+			CompressionLevel:   cfg.CompressionLevel,
+			AgeRecipients:      cfg.AgeRecipients,
+			Repositories:       repos,
+			EnableProgress:     params.EnableProgress,
+			UI:                 params.UI,
+			Exclude:            params.Exclude,
+			SkipErrors:         params.SkipErrors,
+			PreviousSnapshotID: params.PreviousSnapshotID,
 		})
 	}
 }

internal/vaultik/snapshot.go

@@ -240,12 +240,18 @@ func (v *Vaultik) createNamedSnapshot(
 		return err
 	}
 
+	previousSnapshotID, err := v.previousSnapshotID(snapName)
+	if err != nil {
+		return err
+	}
+
 	scanner := v.ScannerFactory(snapshot.ScannerParams{
-		EnableProgress: !opts.Cron,
-		UI:             v.UI,
-		Fs:             v.Fs,
-		Exclude:        v.Config.GetExcludes(snapName),
-		SkipErrors:     opts.SkipErrors,
+		EnableProgress:     !opts.Cron,
+		UI:                 v.UI,
+		Fs:                 v.Fs,
+		Exclude:            v.Config.GetExcludes(snapName),
+		SkipErrors:         opts.SkipErrors,
+		PreviousSnapshotID: previousSnapshotID,
 	})
 
 	snapshotID, err := v.SnapshotManager.CreateSnapshotWithName(
@@ -280,6 +286,24 @@ func (v *Vaultik) createNamedSnapshot(
 	return nil
 }
 
+// previousSnapshotID returns the ID of the most recent completed snapshot
+// named snapName in the local index, or "" when there is none.
+func (v *Vaultik) previousSnapshotID(snapName string) (string, error) {
+	snapshots, err := v.Repositories.Snapshots.ListRecent(v.ctx, listRecentLimit)
+	if err != nil {
+		return "", fmt.Errorf("listing snapshots: %w", err)
+	}
+
+	for _, s := range snapshots {
+		if s.CompletedAt != nil &&
+			parseSnapshotName(s.ID.String(), s.Hostname.String()) == snapName {
+			return s.ID.String(), nil
+		}
+	}
+
+	return "", nil
+}
+
 // resolveSnapshotPaths resolves source directories to absolute paths
 // with symlink resolution.
 func (v *Vaultik) resolveSnapshotPaths(snapName string) ([]string, error) {

internal/vaultik/snapshot_deleted_count_test.go

@@ -0,0 +1,196 @@
+package vaultik_test
+
+import (
+	"bytes"
+	"context"
+	"fmt"
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"sneak.berlin/go/vaultik/internal/config"
+	"sneak.berlin/go/vaultik/internal/database"
+	"sneak.berlin/go/vaultik/internal/log"
+	"sneak.berlin/go/vaultik/internal/storage"
+	"sneak.berlin/go/vaultik/internal/ui"
+	"sneak.berlin/go/vaultik/internal/vaultik"
+)
+
+// These tests cover https://git.eeqj.de/sneak/vaultik/issues/304: a
+// backup counts a file as deleted only when the previous snapshot of
+// the same name had it and it is gone, and never counts an excluded
+// file.
+
+// deletedCountEnv is a backup setup over the source directory src whose
+// user-facing output is kept in out. Each test configures its snapshots
+// with setSnapshot.
+type deletedCountEnv struct {
+	v   *vaultik.Vaultik
+	out *bytes.Buffer
+	src string
+}
+
+// newDeletedCountEnv writes files, keyed by path relative to src.
+func newDeletedCountEnv(t *testing.T, files map[string][]byte) *deletedCountEnv {
+	t.Helper()
+
+	ctx := context.Background()
+	fs := afero.NewOsFs()
+	tempDir := t.TempDir()
+	srcDir := filepath.Join(tempDir, "src")
+
+	for rel, content := range files {
+		path := filepath.Join(srcDir, rel)
+		require.NoError(t, fs.MkdirAll(filepath.Dir(path), 0o755))
+		require.NoError(t, afero.WriteFile(fs, path, content, 0o644))
+	}
+
+	cfg := faultTestConfig()
+	cfg.IndexPath = filepath.Join(tempDir, "index.sqlite")
+	cfg.Snapshots = map[string]config.SnapshotConfig{}
+
+	store, err := storage.NewFileStorer(filepath.Join(tempDir, "remote"))
+	require.NoError(t, err)
+
+	db, err := database.New(ctx, cfg.IndexPath)
+	require.NoError(t, err)
+	t.Cleanup(func() { _ = db.Close() })
+
+	repos := database.NewRepositories(db)
+	out := &bytes.Buffer{}
+	v := newBackupVaultik(ctx, cfg, store, repos, db, fs)
+	v.UI = ui.NewWithColor(out, false)
+
+	return &deletedCountEnv{v: v, out: out, src: srcDir}
+}
+
+// setSnapshot configures the snapshot name to back up the path rel
+// beneath src, with the given excludes.
+func (e *deletedCountEnv) setSnapshot(name, rel string, exclude ...string) {
+	e.v.Config.Snapshots[name] = config.SnapshotConfig{
+		Paths:   []string{filepath.Join(e.src, rel)},
+		Exclude: exclude,
+	}
+}
+
+// backUp runs a backup of the named snapshot and returns its output.
+func (e *deletedCountEnv) backUp(t *testing.T, name string) string {
+	t.Helper()
+
+	e.out.Reset()
+	require.NoError(t, e.v.CreateSnapshot(&vaultik.SnapshotCreateOptions{
+		Snapshots: []string{name},
+	}))
+
+	return e.out.String()
+}
+
+// A file this snapshot excludes is not counted as deleted: neither one
+// that another snapshot backs up, nor one that the previous snapshot of
+// this name had before the exclude was added.
+func TestBackupDoesNotCountExcludedFileAsDeleted(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"top.txt":       []byte("top"),
+		"cache/tmp.bin": []byte("cache"),
+		"photos/a.jpg":  []byte("photo a"),
+		"photos/b.jpg":  []byte("photo b"),
+		"photos/c.jpg":  []byte("photo c"),
+	})
+	env.setSnapshot("photos", "photos")
+	env.setSnapshot("home", "", "/photos")
+
+	env.backUp(t, "photos")
+	assert.Contains(t, env.backUp(t, "home"), filesLine(2, 2, 0))
+
+	env.setSnapshot("home", "", "/photos", "/cache")
+	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
+}
+
+// A file inside a directory that an exclude added after a backup
+// matches is not counted as deleted, though the pattern matches only the
+// directory.
+func TestBackupDoesNotCountFileInExcludedDirectoryAsDeleted(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"top.txt":                 []byte("top"),
+		"app/node_modules/dep.js": []byte("dep"),
+	})
+	env.setSnapshot("home", "")
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(2, 2, 0))
+
+	env.setSnapshot("home", "", "**/node_modules")
+	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
+}
+
+// A backup counts only files that the previous snapshot of its own name
+// had, not one that a later snapshot of another name over the same path
+// had and that is since removed.
+func TestBackupIgnoresSnapshotOfAnotherName(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"kept.txt": []byte("kept"),
+	})
+	env.setSnapshot("home", "")
+	env.setSnapshot("other", "")
+
+	env.backUp(t, "home")
+
+	// Snapshot start times are kept in whole seconds: wait so that other's
+	// snapshot is strictly the most recent.
+	time.Sleep(time.Second)
+
+	extra := filepath.Join(env.src, "extra.txt")
+	require.NoError(t, os.WriteFile(extra, []byte("extra"), 0o600))
+	env.backUp(t, "other")
+	require.NoError(t, os.Remove(extra))
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
+}
+
+// A file removed from disk is counted as deleted by the next backup of
+// the snapshot that had it, and not by any later backup of that
+// snapshot, nor by the first backup of another name over the same path.
+func TestBackupCountsDeletedFileOnce(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	aContent := bytes.Repeat([]byte("a"), 1000)
+	bContent := bytes.Repeat([]byte("b"), 2000)
+	keptContent := bytes.Repeat([]byte("k"), 500)
+
+	env := newDeletedCountEnv(t, map[string][]byte{
+		"a.txt":    aContent,
+		"b.txt":    bContent,
+		"kept.txt": keptContent,
+	})
+	env.setSnapshot("home", "")
+	env.setSnapshot("other", "")
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(3, 3, 0))
+
+	require.NoError(t, os.Remove(filepath.Join(env.src, "a.txt")))
+	require.NoError(t, os.Remove(filepath.Join(env.src, "b.txt")))
+
+	summary := env.backUp(t, "home")
+	assert.Contains(t, summary,
+		"Files: 1 examined, 0 backed up, 1 unchanged, 2 deleted.")
+	assert.Contains(t, summary,
+		fmt.Sprintf("Data: %s total (%s backed up), %s deleted.",
+			env.v.UI.Size(int64(len(keptContent))), env.v.UI.Size(0),
+			env.v.UI.Size(int64(len(aContent)+len(bContent)))))
+
+	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
+	assert.Contains(t, env.backUp(t, "other"), filesLine(1, 0, 1))
+}