Make remote nuke delete leftover .partial uploads (closes #281)

The file and rclone listings skip an object whose name ends in
`.partial`, the temporary name a `file://` or rclone upload writes
before moving the object into place. `remote nuke` deletes only what
the listings return, so it left the `.partial` objects killed uploads
leave behind and still reported the destination store empty.

Storer gains DeletePartialUploads. The file and rclone backends remove
every `.partial` object under the prefix; S3 has none to remove, since
it shows an object only once its upload completes. `remote nuke` calls
it for `metadata/` and `blobs/` as its last step.

Empty directories under a `file://` destination are still left behind.

Model: opus-5-5

TODO.md

@@ -22,6 +22,22 @@ the tag exists and is exercised; what is left is merging `next` to
 
 # Completed Steps
 
+- 2026-10-08: Made `remote nuke` delete the `.partial` files that
+  uploads cut off part-way leave on the destination store
+  ([issue #281](https://git.eeqj.de/sneak/vaultik/issues/281)). The
+  file and rclone listings skip such a file, so the command left it in
+  place and still reported the store empty. It now removes them under
+  `metadata/` and `blobs/` as its last step.
+
+- 2026-10-08: Counted a file that a backup could not store as failed
+  ([issue #280](https://git.eeqj.de/sneak/vaultik/issues/280)). A file
+  that phase 1 counted and phase 2 could not open, because it was
+  unreadable under `--skip-errors` or removed in between, was reported
+  in the summary as unchanged with its bytes as backed up, and the
+  `snapshots` row's `file_count` and `total_size` included it. The
+  summary now counts it as failed, and its data total and the row leave
+  it out.
+
 - 2026-10-08: Made `remote info` report a snapshot's blob count and
   blob size as unknown when its manifest cannot be read
   ([issue #272](https://git.eeqj.de/sneak/vaultik/issues/272)). The

internal/snapshot/scanner.go

@@ -133,10 +133,13 @@ type ScannerConfig struct {
 
 // ScanResult contains the results of a scan operation. Files and bytes
 // are counted per file: BytesScanned is the size of the new and changed
-// files, BytesSkipped that of the unchanged ones.
+// files, BytesSkipped that of the unchanged ones. FilesFailed counts the
+// new and changed files that phase 2 could not store; FilesScanned
+// includes them and BytesScanned does not.
 type ScanResult struct {
 	FilesScanned   int
 	FilesSkipped   int
+	FilesFailed    int
 	FilesDeleted   int
 	BytesScanned   int64
 	BytesSkipped   int64
@@ -1365,7 +1368,7 @@ func (s *Scanner) processFileWithErrorHandling(
 			log.Warn("File was deleted during backup, skipping",
 				"path", fileToProcess.Path)
 
-			result.FilesSkipped++
+			countFailedFile(fileToProcess, result)
 
 			return true, nil
 		}
@@ -1376,7 +1379,7 @@ func (s *Scanner) processFileWithErrorHandling(
 			s.ui.Errorf("Failed to process %s: %v. Skipping (--skip-errors).",
 				s.ui.Path(fileToProcess.Path), err)
 
-			result.FilesSkipped++
+			countFailedFile(fileToProcess, result)
 
 			return true, nil
 		}
@@ -1387,6 +1390,18 @@ func (s *Scanner) processFileWithErrorHandling(
 	return false, nil
 }
 
+// countFailedFile counts a file that phase 2 could not store as failed
+// and takes its size back out of BytesScanned, where phase 1 put it.
+// Phase 1 counts no directories, so a directory is not counted here.
+func countFailedFile(fileToProcess *FileToProcess, result *ScanResult) {
+	if fileToProcess.FileInfo.IsDir() {
+		return
+	}
+
+	result.FilesFailed++
+	result.BytesScanned -= fileToProcess.FileInfo.Size()
+}
+
 // printProcessingProgress prints a periodic progress line during the process phase,
 // showing files processed, bytes transferred, throughput, and ETA
 func (s *Scanner) printProcessingProgress(

internal/snapshot/snapshot.go

@@ -892,7 +892,7 @@ func (sm *SnapshotManager) getFileSize(path string) int64 {
 // BackupStats contains statistics from a backup operation
 type BackupStats struct {
 	FilesScanned  int
-	TotalSize     int64 // Total size of all files examined
+	TotalSize     int64 // Total size of the files in the snapshot
 	ChunksCreated int
 	BlobsCreated  int
 	BytesUploaded int64

internal/storage/faultstore/faultstore.go

@@ -171,6 +171,11 @@ func (f *Storer) ListStream(
 	return f.inner.ListStream(ctx, prefix)
 }
 
+// DeletePartialUploads delegates unchanged.
+func (f *Storer) DeletePartialUploads(ctx context.Context, prefix string) error {
+	return f.inner.DeletePartialUploads(ctx, prefix)
+}
+
 // Info delegates unchanged.
 func (f *Storer) Info() storage.Info {
 	return f.inner.Info()

internal/storage/file.go

@@ -242,6 +242,42 @@ func (f *FileStorer) ListStream(ctx context.Context, prefix string) <-chan Objec
 	return ch
 }
 
+// DeletePartialUploads removes every file under prefix whose name ends in
+// tempSuffix. A missing prefix has none to remove.
+func (f *FileStorer) DeletePartialUploads(ctx context.Context, prefix string) error {
+	basePath := f.fullPath(prefix)
+
+	exists, err := afero.Exists(f.fs, basePath)
+	if err != nil {
+		return fmt.Errorf("checking path: %w", err)
+	}
+
+	if !exists {
+		return nil
+	}
+
+	err = afero.Walk(f.fs, basePath, func(path string, info os.FileInfo, err error) error {
+		if err != nil {
+			return err
+		}
+
+		if ctx.Err() != nil {
+			return ctx.Err()
+		}
+
+		if info.IsDir() || !strings.HasSuffix(info.Name(), tempSuffix) {
+			return nil
+		}
+
+		return f.fs.Remove(path)
+	})
+	if err != nil {
+		return fmt.Errorf("walking directory: %w", err)
+	}
+
+	return nil
+}
+
 // Info returns human-readable storage location information.
 func (f *FileStorer) Info() Info {
 	return Info{

internal/storage/file_atomic_test.go

@@ -120,3 +120,45 @@ func TestFileStorer_ListSkipsPartialFiles(t *testing.T) {
 		t.Fatalf("ListStream should return only the real key, got %v", streamed)
 	}
 }
+
+// TestFileStorer_DeletePartialUploads checks that a leftover temp file is
+// removed and the object at the real key is kept.
+func TestFileStorer_DeletePartialUploads(t *testing.T) {
+	t.Parallel()
+
+	base := t.TempDir()
+
+	f, err := storage.NewFileStorer(base)
+	if err != nil {
+		t.Fatalf("NewFileStorer: %v", err)
+	}
+
+	ctx := context.Background()
+
+	err = f.Put(ctx, testBlobKey, strings.NewReader("blob-bytes"))
+	if err != nil {
+		t.Fatalf("Put: %v", err)
+	}
+
+	leftover := filepath.Join(base, testBlobKey+"-123456.partial")
+
+	err = os.WriteFile(leftover, []byte("half"), 0o600)
+	if err != nil {
+		t.Fatalf("writing leftover temp file: %v", err)
+	}
+
+	err = f.DeletePartialUploads(ctx, "blobs/")
+	if err != nil {
+		t.Fatalf("DeletePartialUploads: %v", err)
+	}
+
+	_, err = os.Stat(leftover)
+	if !os.IsNotExist(err) {
+		t.Errorf("leftover temp file was not removed: %v", err)
+	}
+
+	_, err = f.Stat(ctx, testBlobKey)
+	if err != nil {
+		t.Errorf("Stat of the real key: %v", err)
+	}
+}

internal/storage/rclone.go

@@ -213,6 +213,31 @@ func (r *RcloneStorer) ListStream(
 	return ch
 }
 
+// DeletePartialUploads removes every object under prefix whose name ends
+// in tempSuffix.
+func (r *RcloneStorer) DeletePartialUploads(ctx context.Context, prefix string) error {
+	var partial []fs.Object
+
+	err := operations.ListFn(ctx, r.fsys, func(obj fs.Object) {
+		key := obj.Remote()
+		if strings.HasPrefix(key, prefix) && strings.HasSuffix(key, tempSuffix) {
+			partial = append(partial, obj)
+		}
+	})
+	if err != nil {
+		return fmt.Errorf("listing objects: %w", err)
+	}
+
+	for _, obj := range partial {
+		err = obj.Remove(ctx)
+		if err != nil {
+			return fmt.Errorf("removing object: %w", err)
+		}
+	}
+
+	return nil
+}
+
 // Info returns human-readable storage location information.
 func (r *RcloneStorer) Info() Info {
 	location := r.remote

internal/storage/rclone_test.go

@@ -198,6 +198,47 @@ func TestRcloneStorerListSkipsPartialFiles(t *testing.T) {
 	}
 }
 
+// TestRcloneStorerDeletePartialUploads checks that a temporary file left
+// by a killed upload is removed and the object at the real key is kept.
+//
+//nolint:paralleltest // NewRcloneStorer installs the process-global rclone config
+func TestRcloneStorerDeletePartialUploads(t *testing.T) {
+	dir := t.TempDir()
+	ctx := context.Background()
+
+	s, err := storage.NewRcloneStorer(ctx, ":local", dir)
+	if err != nil {
+		t.Fatalf("NewRcloneStorer: %v", err)
+	}
+
+	err = s.Put(ctx, testBlobKey, strings.NewReader("blob-bytes"))
+	if err != nil {
+		t.Fatalf("Put: %v", err)
+	}
+
+	leftover := filepath.Join(dir, testBlobKey+"-123456.partial")
+
+	err = os.WriteFile(leftover, []byte("half"), 0o600)
+	if err != nil {
+		t.Fatalf("writing leftover temp file: %v", err)
+	}
+
+	err = s.DeletePartialUploads(ctx, "blobs/")
+	if err != nil {
+		t.Fatalf("DeletePartialUploads: %v", err)
+	}
+
+	_, err = os.Stat(leftover)
+	if !os.IsNotExist(err) {
+		t.Errorf("leftover temp file was not removed: %v", err)
+	}
+
+	_, err = s.Stat(ctx, testBlobKey)
+	if err != nil {
+		t.Errorf("Stat of the real key: %v", err)
+	}
+}
+
 // newRcloneStorerOnWrappedLocal registers name as rclone's local backend
 // wrapped by wrap, and builds an rclone backend on it rooted at a fresh
 // temp directory. wrap changes the features the local backend reports, so

internal/storage/s3.go

@@ -99,6 +99,12 @@ func (s *S3Storer) ListStream(ctx context.Context, prefix string) <-chan ObjectI
 	return ch
 }
 
+// DeletePartialUploads has nothing to remove: S3 shows an object only once
+// its upload has completed, so an upload cut off part-way leaves none.
+func (s *S3Storer) DeletePartialUploads(_ context.Context, _ string) error {
+	return nil
+}
+
 // Info returns human-readable storage location information.
 func (s *S3Storer) Info() Info {
 	return Info{

internal/storage/storer.go

@@ -71,6 +71,12 @@ type Storer interface {
 	// If an error occurs during listing, the final item will have Err set.
 	ListStream(ctx context.Context, prefix string) <-chan ObjectInfo
 
+	// DeletePartialUploads removes every object under prefix that an
+	// upload cut off part-way left under a temporary name ending in
+	// `.partial`. The file and rclone backends' List and ListStream skip
+	// such an object.
+	DeletePartialUploads(ctx context.Context, prefix string) error
+
 	// Info returns human-readable storage location information.
 	Info() Info
 }

internal/vaultik/destination_validation_test.go

@@ -257,6 +257,10 @@ func (s *stubLister) List(_ context.Context, _ string) ([]string, error) {
 	return nil, errStubUnused
 }
 
+func (s *stubLister) DeletePartialUploads(_ context.Context, _ string) error {
+	return errStubUnused
+}
+
 func (s *stubLister) Info() storage.Info {
 	return storage.Info{}
 }

internal/vaultik/integration_test.go

@@ -155,6 +155,12 @@ func (m *MockStorer) ListStream(
 	return ch
 }
 
+// DeletePartialUploads has nothing to remove: Put stores each object
+// under its key at once.
+func (m *MockStorer) DeletePartialUploads(_ context.Context, _ string) error {
+	return nil
+}
+
 func (m *MockStorer) Info() storage.Info {
 	return storage.Info{
 		Type:     "mock",

internal/vaultik/nuke_remote_test.go

@@ -0,0 +1,50 @@
+package vaultik_test
+
+import (
+	"context"
+	"io/fs"
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"sneak.berlin/go/vaultik/internal/log"
+)
+
+// TestNukeRemoteLeavesNoFiles checks that remote nuke leaves no file
+// under a file:// destination, including the `.partial` file an upload
+// killed part-way leaves next to where its blob would have been.
+func TestNukeRemoteLeavesNoFiles(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	ctx := context.Background()
+	storeDir := filepath.Join(t.TempDir(), "store")
+	v, _, _ := backUpToFileDestination(ctx, t, storeDir)
+
+	hash := testBlobHashA
+	leftover := filepath.Join(storeDir, "blobs", hash[:2], hash[2:4],
+		hash+"-123456.partial")
+	require.NoError(t, os.MkdirAll(filepath.Dir(leftover), 0o750))
+	require.NoError(t, os.WriteFile(leftover, []byte("half a blob"), 0o600))
+
+	require.NoError(t, v.NukeRemote(true))
+
+	var files []string
+
+	err := filepath.WalkDir(storeDir,
+		func(path string, entry fs.DirEntry, err error) error {
+			if err != nil {
+				return err
+			}
+
+			if !entry.IsDir() {
+				files = append(files, path)
+			}
+
+			return nil
+		})
+	require.NoError(t, err)
+	assert.Empty(t, files)
+}

internal/vaultik/prune.go

@@ -24,8 +24,9 @@ var errNukeRequiresForce = errors.New(
 const metadataDirName = "metadata"
 
 // NukeRemote deletes every snapshot's metadata and every blob from remote
-// storage. After this returns successfully the bucket prefix is empty and
+// storage, along with any object an upload cut off part-way left under a
-// the next backup starts from scratch.
+// temporary `.partial` name. After this returns successfully the bucket
+// prefix is empty and the next backup starts from scratch.
 //
 // Refuses to run unless force is true. The caller is responsible for
 // confirming with the user.
@@ -48,6 +49,15 @@ func (v *Vaultik) NukeRemote(force bool) error {
 		return fmt.Errorf("pruning blobs: %w", err)
 	}
 
+	// The file and rclone listings skip `.partial` objects, so the two
+	// steps above never delete them.
+	for _, prefix := range []string{"metadata/", "blobs/"} {
+		err = v.Storage.DeletePartialUploads(v.ctx, prefix)
+		if err != nil {
+			return fmt.Errorf("deleting partial uploads: %w", err)
+		}
+	}
+
 	v.UI.Completef("Backup destination store is now empty.")
 
 	return nil

internal/vaultik/remove_snapshot_test.go

@@ -125,6 +125,12 @@ func (s *testStorer) ListStream(
 	return ch
 }
 
+// DeletePartialUploads has nothing to remove: Put stores each object
+// under its key at once.
+func (s *testStorer) DeletePartialUploads(_ context.Context, _ string) error {
+	return nil
+}
+
 func (s *testStorer) Info() storage.Info {
 	return storage.Info{
 		Type:     testLabel,

internal/vaultik/snapshot.go

@@ -185,6 +185,7 @@ type snapshotStats struct {
 	totalBlobs         int
 	totalBytesSkipped  int64
 	totalFilesSkipped  int
+	totalFilesFailed   int
 	totalFilesDeleted  int
 	totalBytesDeleted  int64
 	totalBytesUploaded int64
@@ -315,6 +316,7 @@ func (v *Vaultik) scanAllDirectories(
 		stats.totalChunks += result.ChunksCreated
 		stats.totalBlobs += result.BlobsCreated
 		stats.totalFilesSkipped += result.FilesSkipped
+		stats.totalFilesFailed += result.FilesFailed
 		stats.totalBytesSkipped += result.BytesSkipped
 		stats.totalFilesDeleted += result.FilesDeleted
 		stats.totalBytesDeleted += result.BytesDeleted
@@ -326,6 +328,7 @@ func (v *Vaultik) scanAllDirectories(
 			"path", dir,
 			"files", result.FilesScanned,
 			"files_skipped", result.FilesSkipped,
+			"files_failed", result.FilesFailed,
 			"bytes", result.BytesScanned,
 			"bytes_skipped", result.BytesSkipped,
 			"chunks", result.ChunksCreated,
@@ -359,9 +362,11 @@ func (v *Vaultik) finalizeSnapshotMetadata(
 		return fmt.Errorf("getting snapshot blob sizes: %w", err)
 	}
 
+	// file_count and total_size leave out the files that could not be
+	// stored; stats.totalBytes already does.
 	extStats := snapshot.ExtendedBackupStats{
 		BackupStats: snapshot.BackupStats{
-			FilesScanned:  stats.totalFiles,
+			FilesScanned:  stats.totalFiles - stats.totalFilesFailed,
 			TotalSize:     stats.totalBytes + stats.totalBytesSkipped,
 			ChunksCreated: stats.totalChunks,
 			BlobsCreated:  stats.totalBlobs,
@@ -409,7 +414,8 @@ func (v *Vaultik) printSnapshotSummary(
 	snapshotID string, startTime time.Time, stats *snapshotStats,
 ) {
 	snapshotDuration := time.Since(startTime)
-	totalFilesChanged := stats.totalFiles - stats.totalFilesSkipped
+	totalFilesChanged := stats.totalFiles - stats.totalFilesSkipped -
+		stats.totalFilesFailed
 	totalBytesAll := stats.totalBytes + stats.totalBytesSkipped
 
 	var compressionRatio float64
@@ -426,6 +432,10 @@ func (v *Vaultik) printSnapshotSummary(
 		v.UI.Count(stats.totalFiles),
 		v.UI.Count(totalFilesChanged),
 		v.UI.Count(stats.totalFilesSkipped))
+	if stats.totalFilesFailed > 0 {
+		filesMsg += fmt.Sprintf(", %s failed", v.UI.Count(stats.totalFilesFailed))
+	}
+
 	if stats.totalFilesDeleted > 0 {
 		filesMsg += fmt.Sprintf(", %s deleted", v.UI.Count(stats.totalFilesDeleted))
 	}

internal/vaultik/snapshot_failed_file_test.go

@@ -0,0 +1,123 @@
+package vaultik_test
+
+import (
+	"bytes"
+	"context"
+	"fmt"
+	"os"
+	"path/filepath"
+	"testing"
+
+	"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"
+)
+
+// openFailFs is the real filesystem, except that opening path fails
+// with err. Phase 1 of a backup only lstats a file, so it still counts
+// path; phase 2 is the first to open it.
+type openFailFs struct {
+	afero.OsFs
+
+	path string
+	err  error
+}
+
+//nolint:ireturn // afero.Fs.Open is defined to return the interface.
+func (f *openFailFs) Open(name string) (afero.File, error) {
+	if name == f.path {
+		return nil, &os.PathError{Op: "open", Path: name, Err: f.err}
+	}
+
+	return f.OsFs.Open(name)
+}
+
+// A file that phase 2 cannot open is reported as failed, not as
+// unchanged, and neither the summary's data total nor the snapshots row
+// counts it. See https://git.eeqj.de/sneak/vaultik/issues/280.
+func TestSnapshotSummaryCountsFileNotStoredAsFailed(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	tests := []struct {
+		name       string
+		openErr    error
+		skipErrors bool
+	}{
+		// What a normal user gets opening a file with mode 000.
+		{name: "unopenable under skip-errors",
+			openErr: os.ErrPermission, skipErrors: true},
+		// What opening a file removed after phase 1 gives.
+		{name: "removed between the phases",
+			openErr: os.ErrNotExist, skipErrors: false},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+
+			ctx := context.Background()
+
+			// The scan walks the source path with symlinks resolved, so
+			// failedPath must be spelled the same way to match.
+			tempDir, err := filepath.EvalSymlinks(t.TempDir())
+			require.NoError(t, err)
+
+			srcDir := filepath.Join(tempDir, "src")
+			failedPath := filepath.Join(srcDir, "failed.txt")
+			storedContent := []byte("this file is backed up")
+			storedSize := int64(len(storedContent))
+
+			fs := &openFailFs{path: failedPath, err: tt.openErr}
+			require.NoError(t, fs.MkdirAll(srcDir, 0o755))
+			require.NoError(t, afero.WriteFile(fs,
+				filepath.Join(srcDir, "stored.txt"), storedContent, 0o644))
+			require.NoError(t, afero.WriteFile(fs,
+				failedPath, []byte("this file cannot be opened"), 0o644))
+
+			cfg := faultTestConfig()
+			cfg.IndexPath = filepath.Join(tempDir, "index.sqlite")
+			cfg.Snapshots = map[string]config.SnapshotConfig{
+				"src": {Paths: []string{srcDir}},
+			}
+
+			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)
+
+			require.NoError(t, v.CreateSnapshot(&vaultik.SnapshotCreateOptions{
+				SkipErrors: tt.skipErrors,
+				Snapshots:  []string{"src"},
+			}))
+
+			summary := out.String()
+			assert.Contains(t, summary,
+				"Files: 2 examined, 1 backed up, 0 unchanged, 1 failed.")
+			assert.Contains(t, summary,
+				fmt.Sprintf("Data: %s total (%s backed up).",
+					v.UI.Size(storedSize), v.UI.Size(storedSize)))
+
+			snap, err := repos.Snapshots.GetByID(ctx,
+				localSnapshotID(ctx, t, repos, "src"))
+			require.NoError(t, err)
+			require.NotNil(t, snap)
+
+			assert.Equal(t, int64(1), snap.FileCount)
+			assert.Equal(t, storedSize, snap.TotalSize)
+		})
+	}
+}