Re-chunk a known file whose chunks no uploaded blob holds (closes #214)

File rows are shared by every snapshot and updated in place, while a
blob row is deleted once no snapshot references it. Removing the newest
snapshot, or the prune after an interrupted run, could drop the only
blob holding a changed file's current chunks while an older snapshot
kept the file row. The next backup compared metadata only, skipped the
file, and completed a snapshot that could not restore it.

The scanner now loads the IDs of known files that list a chunk no
uploaded blob holds and re-chunks them even when their metadata is
unchanged.

The tests append to a file, so the file keeps its first chunk in a blob
the first snapshot still references. Each backup run gets its own
snapshot name, so the second-precision snapshot IDs differ without
sleeping.

Model: opus-5-5

internal/snapshot/scanner.go

@@ -73,6 +73,11 @@ type Scanner struct {
 	knownChunks   map[string]struct{}
 	knownChunksMu sync.RWMutex
 
+	// filesToRechunk holds the IDs of known files that list a chunk no
+	// uploaded blob holds; they are re-chunked even when their metadata
+	// is unchanged.
+	filesToRechunk map[types.FileID]struct{}
+
 	// Pending chunk hashes - chunks that have been added to packer but not
 	// yet committed to DB. When a blob finalizes, the committed chunks are
 	// removed from this set.
@@ -325,9 +330,42 @@ func (s *Scanner) loadDatabaseState(
 	s.ui.Completef("Loaded %s known chunks from local index database.",
 		s.ui.Count(len(s.knownChunks)))
 
+	err = s.loadFilesToRechunk(ctx, path)
+	if err != nil {
+		return nil, fmt.Errorf("loading files to re-chunk: %w", err)
+	}
+
 	return knownFiles, nil
 }
 
+// loadFilesToRechunk loads the IDs of known files under path that list a
+// chunk no uploaded blob holds. A file row is shared by every snapshot
+// that lists the file and is updated in place when the file changes,
+// while a blob row is deleted once no snapshot references it. Removing
+// the only snapshot that references a changed file's current blob
+// therefore leaves an older snapshot keeping a file row whose metadata
+// matches the disk while no blob the local index records as uploaded
+// holds its chunks, so a new snapshot cannot reference them. The dropped
+// blob can still be in remote storage until prune removes it.
+func (s *Scanner) loadFilesToRechunk(ctx context.Context, path string) error {
+	ids, err := s.repos.Files.ListIDsWithChunksNotInUploadedBlobs(ctx, path)
+	if err != nil {
+		return fmt.Errorf("listing files: %w", err)
+	}
+
+	s.filesToRechunk = make(map[types.FileID]struct{}, len(ids))
+	for _, id := range ids {
+		s.filesToRechunk[id] = struct{}{}
+	}
+
+	if len(ids) > 0 {
+		log.Info("Re-chunking known files whose chunks are not all "+
+			"in uploaded blobs", "files", len(ids))
+	}
+
+	return nil
+}
+
 // repairInterruptedBlobs discards blob rows left by a previous run whose
 // upload never completed. Such a blob has its chunks, blob_chunks, and
 // blobs rows committed to the local index before the upload is attempted,
@@ -1208,6 +1246,11 @@ func (s *Scanner) checkFileInMemory(
 		return file, true
 	}
 
+	// No uploaded blob holds one of its chunks (see loadFilesToRechunk)
+	if _, rechunk := s.filesToRechunk[fileID]; rechunk {
+		return file, true
+	}
+
 	// Check if file has changed
 	if existingFile.Size != file.Size ||
 		existingFile.MTime.Unix() != file.MTime.Unix() ||