Trust only uploaded blobs for deduplication (closes #148)

An interrupted blob upload left the blob's chunks, blob_chunks, and blobs rows committed before the upload was attempted, so a later run deduplicated against data that never reached storage and produced a snapshot that reported success but could not be restored.

Fix (issue option b): a chunk counts as known only when a blob holding it has uploaded_ts set, and each run drops un-uploaded blob rows and the chunks they orphan at startup, so the affected data is re-chunked and re-uploaded. A blob recorded with no remote backend is marked uploaded so the invariant holds uniformly.

The reproduction is the interrupted-upload test from #72: its t.Skip is removed and it passes against this fix, and this branch's earlier duplicate copy is dropped. The interrupted metadata-export case is split to #177.

Model: opus-4-8

internal/snapshot/scanner.go

@@ -220,7 +220,14 @@ func (s *Scanner) Scan(
 		defer s.progress.Stop()
 	}
 
-	// Phase 0: Load known files and chunks from database into memory for fast lookup
+	// Phase 0: Repair any state left by an interrupted previous run, then
+	// load known files and chunks from the database into memory for fast
+	// lookup.
+	err := s.repairInterruptedBlobs(ctx)
+	if err != nil {
+		return nil, err
+	}
+
 	knownFiles, err := s.loadDatabaseState(ctx, path)
 	if err != nil {
 		return nil, err
@@ -317,6 +324,38 @@ func (s *Scanner) loadDatabaseState(
 	return knownFiles, 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,
+// so a crash or dropped connection mid-upload leaves them behind while the
+// data never reaches remote storage. Deduplicating against those chunks on
+// a later run would produce a snapshot that reports success but cannot be
+// restored. Dropping the un-uploaded blobs (their blob_chunks cascade) and
+// then any chunks left unreferenced forces the affected data to be
+// re-chunked and re-uploaded this run. A blob is attached to a snapshot
+// only once its upload is recorded, so this never touches a completed
+// snapshot's data.
+func (s *Scanner) repairInterruptedBlobs(ctx context.Context) error {
+	removed, err := s.repos.Blobs.DeleteUnuploaded(ctx)
+	if err != nil {
+		return fmt.Errorf("removing un-uploaded blob records: %w", err)
+	}
+
+	if removed == 0 {
+		return nil
+	}
+
+	log.Warn("Discarded blob records from an interrupted previous run; "+
+		"their data will be re-uploaded", "blobs", removed)
+
+	err = s.repos.Chunks.DeleteOrphaned(ctx)
+	if err != nil {
+		return fmt.Errorf("removing orphaned chunks: %w", err)
+	}
+
+	return nil
+}
+
 // summarizeScanPhase calculates total size to process, updates progress tracking,
 // and prints the scan phase summary with file counts and sizes
 func (s *Scanner) summarizeScanPhase(
@@ -392,11 +431,14 @@ func (s *Scanner) loadKnownFiles(
 	return result, nil
 }
 
-// loadKnownChunks loads all known chunk hashes from the database into a
-// map for fast lookup. This avoids per-chunk database queries during file
-// processing.
+// loadKnownChunks loads the chunk hashes safe to deduplicate against into
+// an in-memory map for fast lookup, avoiding per-chunk database queries
+// during file processing. Only chunks held by a blob whose upload
+// completed are loaded: a chunk left behind by an interrupted upload
+// refers to data that never reached remote storage, and deduplicating
+// against it would silently produce an unrestorable snapshot.
 func (s *Scanner) loadKnownChunks(ctx context.Context) error {
-	chunks, err := s.repos.Chunks.List(ctx)
+	chunks, err := s.repos.Chunks.ListInUploadedBlobs(ctx)
 	if err != nil {
 		return fmt.Errorf("listing chunks: %w", err)
 	}
@@ -1401,7 +1443,17 @@ func (s *Scanner) finalizeProcessPhase(ctx context.Context, result *ScanResult)
 				return fmt.Errorf("parsing blob ID: %w", err)
 			}
 
+			// With no remote backend the blob's lifecycle ends here, so
+			// mark it uploaded in the same transaction that attaches it to
+			// the snapshot. This keeps the invariant that any blob a
+			// snapshot references has uploaded_ts set, so deduplication and
+			// interrupted-run repair treat these blobs as trustworthy.
 			err = s.repos.WithTx(ctx, func(ctx context.Context, tx *sql.Tx) error {
+				err := s.repos.Blobs.UpdateUploaded(ctx, tx, b.ID)
+				if err != nil {
+					return fmt.Errorf("marking blob uploaded: %w", err)
+				}
+
 				return s.repos.Snapshots.AddBlob(ctx, tx, s.snapshotID, blobID,
 					types.BlobHash(b.Hash))
 			})