Implement multi-repo hydration layer with mtime caching (bd-307)

- Add repo_mtimes table to track JSONL file modification times
- Implement HydrateFromMultiRepo() with mtime-based skip optimization
- Support tilde expansion for repo paths in config
- Add source_repo column via migration (not in base schema)
- Fix schema to allow migration on existing databases
- Comprehensive test coverage for hydration logic
- Resurrect missing parent issues bd-cb64c226 and bd-cbed9619

Implementation:
- internal/storage/sqlite/multirepo.go - Core hydration logic
- internal/storage/sqlite/multirepo_test.go - Test coverage
- docs/MULTI_REPO_HYDRATION.md - Documentation

Schema changes:
- source_repo column added via migration only (not base schema)
- repo_mtimes table for mtime caching
- All SELECT queries updated to include source_repo

Database recovery:
- Restored from 17 to 285 issues
- Created placeholder parents for orphaned hierarchical children

Amp-Thread-ID: https://ampcode.com/threads/T-faa1339a-14b2-426c-8e18-aa8be6f5cde6
Co-authored-by: Amp <amp@ampcode.com>

internal/storage/sqlite/sqlite.go

@@ -88,10 +88,22 @@ func New(path string) (*SQLiteStorage, error) {
 		}
 	}
 
-	return &SQLiteStorage{
+	storage := &SQLiteStorage{
 		db:     db,
 		dbPath: absPath,
-	}, nil
+	}
+
+	// Hydrate from multi-repo config if configured (bd-307)
+	// Skip for in-memory databases (used in tests)
+	if path != ":memory:" {
+		ctx := context.Background()
+		_, err := storage.HydrateFromMultiRepo(ctx)
+		if err != nil {
+			return nil, fmt.Errorf("failed to hydrate from multi-repo: %w", err)
+		}
+	}
+
+	return storage, nil
 }
 
 // REMOVED (bd-8e05): getNextIDForPrefix and AllocateNextID - sequential ID generation
@@ -231,6 +243,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 	var externalRef sql.NullString
 	var compactedAt sql.NullTime
 	var originalSize sql.NullInt64
+	var sourceRepo sql.NullString
 
 	var contentHash sql.NullString
 	var compactedAtCommit sql.NullString
@@ -238,7 +251,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 		SELECT id, content_hash, title, description, design, acceptance_criteria, notes,
 		       status, priority, issue_type, assignee, estimated_minutes,
 		       created_at, updated_at, closed_at, external_ref,
-		       compaction_level, compacted_at, compacted_at_commit, original_size
+		       compaction_level, compacted_at, compacted_at_commit, original_size, source_repo
 		FROM issues
 		WHERE id = ?
 	`, id).Scan(
@@ -246,7 +259,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 		&issue.AcceptanceCriteria, &issue.Notes, &issue.Status,
 		&issue.Priority, &issue.IssueType, &assignee, &estimatedMinutes,
 		&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef,
-		&issue.CompactionLevel, &compactedAt, &compactedAtCommit, &originalSize,
+		&issue.CompactionLevel, &compactedAt, &compactedAtCommit, &originalSize, &sourceRepo,
 	)
 
 	if err == sql.ErrNoRows {
@@ -281,6 +294,9 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 	if originalSize.Valid {
 		issue.OriginalSize = int(originalSize.Int64)
 	}
+	if sourceRepo.Valid {
+		issue.SourceRepo = sourceRepo.String
+	}
 
 	// Fetch labels for this issue
 	labels, err := s.GetLabels(ctx, issue.ID)
@@ -1132,7 +1148,7 @@ func (s *SQLiteStorage) SearchIssues(ctx context.Context, query string, filter t
 	querySQL := fmt.Sprintf(`
 		SELECT id, content_hash, title, description, design, acceptance_criteria, notes,
 		       status, priority, issue_type, assignee, estimated_minutes,
-		       created_at, updated_at, closed_at, external_ref
+		       created_at, updated_at, closed_at, external_ref, source_repo
 		FROM issues
 		%s
 		ORDER BY priority ASC, created_at DESC