refactor(sqlite): use withTx helper for remaining transaction entry points (#1276)

Refactors UpdateIssue, CloseIssue, CreateTombstone, and DeleteIssues
to use the withTx helper with BEGIN IMMEDIATE instead of BeginTx.
This completes the GH#1272 fix by ensuring all write transactions
acquire write locks early, preventing deadlocks.

Changes:
- UpdateIssue: now uses withTx and markDirty helper
- CloseIssue: now uses withTx and markDirty helper
- CreateTombstone: now uses withTx and markDirty helper
- DeleteIssues: now uses withTx with dbExecutor interface
- Helper functions (resolveDeleteSet, expandWithDependents,
  validateNoDependents, etc.) changed from *sql.Tx to dbExecutor

This is a P3 follow-up to the P1 sqlite lock fix (PR #1274).

Closes: bd-fgzp

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

internal/storage/sqlite/queries.go

@@ -996,21 +996,7 @@ func (s *SQLiteStorage) UpdateIssue(ctx context.Context, id string, updates map[
 
 	args = append(args, id)
 
-	// Start transaction
-	tx, err := s.db.BeginTx(ctx, nil)
-	if err != nil {
-		return fmt.Errorf("failed to begin transaction: %w", err)
-	}
-	defer func() { _ = tx.Rollback() }()
-
-	// Update issue
-	query := fmt.Sprintf("UPDATE issues SET %s WHERE id = ?", strings.Join(setClauses, ", ")) // #nosec G201 - safe SQL with controlled column names
-	_, err = tx.ExecContext(ctx, query, args...)
-	if err != nil {
-		return fmt.Errorf("failed to update issue: %w", err)
-	}
-
-	// Record event
+	// Prepare event data before transaction
 	oldData, err := json.Marshal(oldIssue)
 	if err != nil {
 		// Fall back to minimal description if marshaling fails
@@ -1023,38 +1009,47 @@ func (s *SQLiteStorage) UpdateIssue(ctx context.Context, id string, updates map[
 	}
 	oldDataStr := string(oldData)
 	newDataStr := string(newData)
-
 	eventType := determineEventType(oldIssue, updates)
-
-	_, err = tx.ExecContext(ctx, `
-		INSERT INTO events (issue_id, event_type, actor, old_value, new_value)
-		VALUES (?, ?, ?, ?, ?)
-	`, id, eventType, actor, oldDataStr, newDataStr)
-	if err != nil {
-		return fmt.Errorf("failed to record event: %w", err)
+	statusChanged := false
+	if _, ok := updates["status"]; ok {
+		statusChanged = true
 	}
 
-	// NOTE: Graph edges now managed via AddDependency() per Decision 004 Phase 4.
-
-	// Mark issue as dirty for incremental export
-	_, err = tx.ExecContext(ctx, `
-		INSERT INTO dirty_issues (issue_id, marked_at)
-		VALUES (?, ?)
-		ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
-	`, id, time.Now())
-	if err != nil {
-		return fmt.Errorf("failed to mark issue dirty: %w", err)
-	}
-
-	// Invalidate blocked issues cache if status changed
-	// Status changes affect which issues are blocked (blockers must be open/in_progress/blocked)
-	if _, statusChanged := updates["status"]; statusChanged {
-		if err := s.invalidateBlockedCache(ctx, tx); err != nil {
-			return fmt.Errorf("failed to invalidate blocked cache: %w", err)
+	// Execute in transaction using BEGIN IMMEDIATE (GH#1272 fix)
+	return s.withTx(ctx, func(conn *sql.Conn) error {
+		// Update issue
+		query := fmt.Sprintf("UPDATE issues SET %s WHERE id = ?", strings.Join(setClauses, ", ")) // #nosec G201 - safe SQL with controlled column names
+		_, err := conn.ExecContext(ctx, query, args...)
+		if err != nil {
+			return fmt.Errorf("failed to update issue: %w", err)
 		}
-	}
 
-	return tx.Commit()
+		// Record event
+		_, err = conn.ExecContext(ctx, `
+			INSERT INTO events (issue_id, event_type, actor, old_value, new_value)
+			VALUES (?, ?, ?, ?, ?)
+		`, id, eventType, actor, oldDataStr, newDataStr)
+		if err != nil {
+			return fmt.Errorf("failed to record event: %w", err)
+		}
+
+		// NOTE: Graph edges now managed via AddDependency() per Decision 004 Phase 4.
+
+		// Mark issue as dirty for incremental export
+		if err := markDirty(ctx, conn, id); err != nil {
+			return fmt.Errorf("failed to mark issue dirty: %w", err)
+		}
+
+		// Invalidate blocked issues cache if status changed
+		// Status changes affect which issues are blocked (blockers must be open/in_progress/blocked)
+		if statusChanged {
+			if err := s.invalidateBlockedCache(ctx, conn); err != nil {
+				return fmt.Errorf("failed to invalidate blocked cache: %w", err)
+			}
+		}
+
+		return nil
+	})
 }
 
 // UpdateIssueID updates an issue ID and all its text fields in a single transaction
@@ -1208,136 +1203,122 @@ func (s *SQLiteStorage) ResetCounter(ctx context.Context, prefix string) error {
 func (s *SQLiteStorage) CloseIssue(ctx context.Context, id string, reason string, actor string, session string) error {
 	now := time.Now()
 
-	// Update with special event handling
-	tx, err := s.db.BeginTx(ctx, nil)
-	if err != nil {
-		return fmt.Errorf("failed to begin transaction: %w", err)
-	}
-	defer func() { _ = tx.Rollback() }()
-
-	// NOTE: close_reason is stored in two places:
-	// 1. issues.close_reason - for direct queries (bd show --json, exports)
-	// 2. events.comment - for audit history (when was it closed, by whom)
-	// Keep both in sync. If refactoring, consider deriving one from the other.
-	result, err := tx.ExecContext(ctx, `
-		UPDATE issues SET status = ?, closed_at = ?, updated_at = ?, close_reason = ?, closed_by_session = ?
-		WHERE id = ?
-	`, types.StatusClosed, now, now, reason, session, id)
-	if err != nil {
-		return fmt.Errorf("failed to close issue: %w", err)
-	}
-
-	rows, err := result.RowsAffected()
-	if err != nil {
-		return fmt.Errorf("failed to get rows affected: %w", err)
-	}
-	if rows == 0 {
-		return fmt.Errorf("issue not found: %s", id)
-	}
-
-	_, err = tx.ExecContext(ctx, `
-		INSERT INTO events (issue_id, event_type, actor, comment)
-		VALUES (?, ?, ?, ?)
-	`, id, types.EventClosed, actor, reason)
-	if err != nil {
-		return fmt.Errorf("failed to record event: %w", err)
-	}
-
-	// Mark issue as dirty for incremental export
-	_, err = tx.ExecContext(ctx, `
-		INSERT INTO dirty_issues (issue_id, marked_at)
-		VALUES (?, ?)
-		ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
-	`, id, time.Now())
-	if err != nil {
-		return fmt.Errorf("failed to mark issue dirty: %w", err)
-	}
-
-	// Invalidate blocked issues cache since status changed to closed
-	// Closed issues don't block others, so this affects blocking calculations
-	if err := s.invalidateBlockedCache(ctx, tx); err != nil {
-		return fmt.Errorf("failed to invalidate blocked cache: %w", err)
-	}
-
-	// Reactive convoy completion: check if any convoys tracking this issue should auto-close
-	// Find convoys that track this issue (convoy.issue_id tracks closed_issue.depends_on_id)
-	// Uses gt:convoy label instead of issue_type for Gas Town separation
-	convoyRows, err := tx.QueryContext(ctx, `
-		SELECT DISTINCT d.issue_id
-		FROM dependencies d
-		JOIN issues i ON d.issue_id = i.id
-		JOIN labels l ON i.id = l.issue_id AND l.label = 'gt:convoy'
-		WHERE d.depends_on_id = ?
-		  AND d.type = ?
-		  AND i.status != ?
-	`, id, types.DepTracks, types.StatusClosed)
-	if err != nil {
-		return fmt.Errorf("failed to find tracking convoys: %w", err)
-	}
-	defer func() { _ = convoyRows.Close() }()
-
-	var convoyIDs []string
-	for convoyRows.Next() {
-		var convoyID string
-		if err := convoyRows.Scan(&convoyID); err != nil {
-			return fmt.Errorf("failed to scan convoy ID: %w", err)
+	// Execute in transaction using BEGIN IMMEDIATE (GH#1272 fix)
+	return s.withTx(ctx, func(conn *sql.Conn) error {
+		// NOTE: close_reason is stored in two places:
+		// 1. issues.close_reason - for direct queries (bd show --json, exports)
+		// 2. events.comment - for audit history (when was it closed, by whom)
+		// Keep both in sync. If refactoring, consider deriving one from the other.
+		result, err := conn.ExecContext(ctx, `
+			UPDATE issues SET status = ?, closed_at = ?, updated_at = ?, close_reason = ?, closed_by_session = ?
+			WHERE id = ?
+		`, types.StatusClosed, now, now, reason, session, id)
+		if err != nil {
+			return fmt.Errorf("failed to close issue: %w", err)
 		}
-		convoyIDs = append(convoyIDs, convoyID)
-	}
-	if err := convoyRows.Err(); err != nil {
-		return fmt.Errorf("convoy rows iteration error: %w", err)
-	}
 
-	// For each convoy, check if all tracked issues are now closed
-	for _, convoyID := range convoyIDs {
-		// Count non-closed tracked issues for this convoy
-		var openCount int
-		err := tx.QueryRowContext(ctx, `
-			SELECT COUNT(*)
+		rows, err := result.RowsAffected()
+		if err != nil {
+			return fmt.Errorf("failed to get rows affected: %w", err)
+		}
+		if rows == 0 {
+			return fmt.Errorf("issue not found: %s", id)
+		}
+
+		_, err = conn.ExecContext(ctx, `
+			INSERT INTO events (issue_id, event_type, actor, comment)
+			VALUES (?, ?, ?, ?)
+		`, id, types.EventClosed, actor, reason)
+		if err != nil {
+			return fmt.Errorf("failed to record event: %w", err)
+		}
+
+		// Mark issue as dirty for incremental export
+		if err := markDirty(ctx, conn, id); err != nil {
+			return fmt.Errorf("failed to mark issue dirty: %w", err)
+		}
+
+		// Invalidate blocked issues cache since status changed to closed
+		// Closed issues don't block others, so this affects blocking calculations
+		if err := s.invalidateBlockedCache(ctx, conn); err != nil {
+			return fmt.Errorf("failed to invalidate blocked cache: %w", err)
+		}
+
+		// Reactive convoy completion: check if any convoys tracking this issue should auto-close
+		// Find convoys that track this issue (convoy.issue_id tracks closed_issue.depends_on_id)
+		// Uses gt:convoy label instead of issue_type for Gas Town separation
+		convoyRows, err := conn.QueryContext(ctx, `
+			SELECT DISTINCT d.issue_id
 			FROM dependencies d
-			JOIN issues i ON d.depends_on_id = i.id
-			WHERE d.issue_id = ?
+			JOIN issues i ON d.issue_id = i.id
+			JOIN labels l ON i.id = l.issue_id AND l.label = 'gt:convoy'
+			WHERE d.depends_on_id = ?
 			  AND d.type = ?
 			  AND i.status != ?
-			  AND i.status != ?
-		`, convoyID, types.DepTracks, types.StatusClosed, types.StatusTombstone).Scan(&openCount)
+		`, id, types.DepTracks, types.StatusClosed)
 		if err != nil {
-			return fmt.Errorf("failed to count open tracked issues for convoy %s: %w", convoyID, err)
+			return fmt.Errorf("failed to find tracking convoys: %w", err)
+		}
+		defer func() { _ = convoyRows.Close() }()
+
+		var convoyIDs []string
+		for convoyRows.Next() {
+			var convoyID string
+			if err := convoyRows.Scan(&convoyID); err != nil {
+				return fmt.Errorf("failed to scan convoy ID: %w", err)
+			}
+			convoyIDs = append(convoyIDs, convoyID)
+		}
+		if err := convoyRows.Err(); err != nil {
+			return fmt.Errorf("convoy rows iteration error: %w", err)
 		}
 
-		// If all tracked issues are closed, auto-close the convoy
-		if openCount == 0 {
-			closeReason := "All tracked issues completed"
-			_, err := tx.ExecContext(ctx, `
-				UPDATE issues SET status = ?, closed_at = ?, updated_at = ?, close_reason = ?
-				WHERE id = ?
-			`, types.StatusClosed, now, now, closeReason, convoyID)
+		// For each convoy, check if all tracked issues are now closed
+		for _, convoyID := range convoyIDs {
+			// Count non-closed tracked issues for this convoy
+			var openCount int
+			err := conn.QueryRowContext(ctx, `
+				SELECT COUNT(*)
+				FROM dependencies d
+				JOIN issues i ON d.depends_on_id = i.id
+				WHERE d.issue_id = ?
+				  AND d.type = ?
+				  AND i.status != ?
+				  AND i.status != ?
+			`, convoyID, types.DepTracks, types.StatusClosed, types.StatusTombstone).Scan(&openCount)
 			if err != nil {
-				return fmt.Errorf("failed to auto-close convoy %s: %w", convoyID, err)
+				return fmt.Errorf("failed to count open tracked issues for convoy %s: %w", convoyID, err)
 			}
 
-			// Record the close event
-			_, err = tx.ExecContext(ctx, `
-				INSERT INTO events (issue_id, event_type, actor, comment)
-				VALUES (?, ?, ?, ?)
-			`, convoyID, types.EventClosed, "system:convoy-completion", closeReason)
-			if err != nil {
-				return fmt.Errorf("failed to record convoy close event: %w", err)
-			}
+			// If all tracked issues are closed, auto-close the convoy
+			if openCount == 0 {
+				closeReason := "All tracked issues completed"
+				_, err := conn.ExecContext(ctx, `
+					UPDATE issues SET status = ?, closed_at = ?, updated_at = ?, close_reason = ?
+					WHERE id = ?
+				`, types.StatusClosed, now, now, closeReason, convoyID)
+				if err != nil {
+					return fmt.Errorf("failed to auto-close convoy %s: %w", convoyID, err)
+				}
 
-			// Mark convoy as dirty
-			_, err = tx.ExecContext(ctx, `
-				INSERT INTO dirty_issues (issue_id, marked_at)
-				VALUES (?, ?)
-				ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
-			`, convoyID, now)
-			if err != nil {
-				return fmt.Errorf("failed to mark convoy dirty: %w", err)
+				// Record the close event
+				_, err = conn.ExecContext(ctx, `
+					INSERT INTO events (issue_id, event_type, actor, comment)
+					VALUES (?, ?, ?, ?)
+				`, convoyID, types.EventClosed, "system:convoy-completion", closeReason)
+				if err != nil {
+					return fmt.Errorf("failed to record convoy close event: %w", err)
+				}
+
+				// Mark convoy as dirty
+				if err := markDirty(ctx, conn, convoyID); err != nil {
+					return fmt.Errorf("failed to mark convoy dirty: %w", err)
+				}
 			}
 		}
-	}
 
-	return tx.Commit()
+		return nil
+	})
 }
 
 // CreateTombstone converts an existing issue to a tombstone record.
@@ -1354,63 +1335,51 @@ func (s *SQLiteStorage) CreateTombstone(ctx context.Context, id string, actor st
 		return fmt.Errorf("issue not found: %s", id)
 	}
 
-	tx, err := s.db.BeginTx(ctx, nil)
-	if err != nil {
-		return fmt.Errorf("failed to begin transaction: %w", err)
-	}
-	defer func() { _ = tx.Rollback() }()
-
 	now := time.Now()
 	originalType := string(issue.IssueType)
 
-	// Convert issue to tombstone
-	// Note: closed_at must be set to NULL because of CHECK constraint:
-	// (status = 'closed') = (closed_at IS NOT NULL)
-	_, err = tx.ExecContext(ctx, `
-		UPDATE issues
-		SET status = ?,
-		    closed_at = NULL,
-		    deleted_at = ?,
-		    deleted_by = ?,
-		    delete_reason = ?,
-		    original_type = ?,
-		    updated_at = ?
-		WHERE id = ?
-	`, types.StatusTombstone, now, actor, reason, originalType, now, id)
-	if err != nil {
-		return fmt.Errorf("failed to create tombstone: %w", err)
-	}
+	// Execute in transaction using BEGIN IMMEDIATE (GH#1272 fix)
+	return s.withTx(ctx, func(conn *sql.Conn) error {
+		// Convert issue to tombstone
+		// Note: closed_at must be set to NULL because of CHECK constraint:
+		// (status = 'closed') = (closed_at IS NOT NULL)
+		_, err := conn.ExecContext(ctx, `
+			UPDATE issues
+			SET status = ?,
+			    closed_at = NULL,
+			    deleted_at = ?,
+			    deleted_by = ?,
+			    delete_reason = ?,
+			    original_type = ?,
+			    updated_at = ?
+			WHERE id = ?
+		`, types.StatusTombstone, now, actor, reason, originalType, now, id)
+		if err != nil {
+			return fmt.Errorf("failed to create tombstone: %w", err)
+		}
 
-	// Record tombstone creation event
-	_, err = tx.ExecContext(ctx, `
-		INSERT INTO events (issue_id, event_type, actor, comment)
-		VALUES (?, ?, ?, ?)
-	`, id, "deleted", actor, reason)
-	if err != nil {
-		return fmt.Errorf("failed to record tombstone event: %w", err)
-	}
+		// Record tombstone creation event
+		_, err = conn.ExecContext(ctx, `
+			INSERT INTO events (issue_id, event_type, actor, comment)
+			VALUES (?, ?, ?, ?)
+		`, id, "deleted", actor, reason)
+		if err != nil {
+			return fmt.Errorf("failed to record tombstone event: %w", err)
+		}
 
-	// Mark issue as dirty for incremental export
-	_, err = tx.ExecContext(ctx, `
-		INSERT INTO dirty_issues (issue_id, marked_at)
-		VALUES (?, ?)
-		ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
-	`, id, now)
-	if err != nil {
-		return fmt.Errorf("failed to mark issue dirty: %w", err)
-	}
+		// Mark issue as dirty for incremental export
+		if err := markDirty(ctx, conn, id); err != nil {
+			return fmt.Errorf("failed to mark issue dirty: %w", err)
+		}
 
-	// Invalidate blocked issues cache since status changed
-	// Tombstone issues don't block others, so this affects blocking calculations
-	if err := s.invalidateBlockedCache(ctx, tx); err != nil {
-		return fmt.Errorf("failed to invalidate blocked cache: %w", err)
-	}
+		// Invalidate blocked issues cache since status changed
+		// Tombstone issues don't block others, so this affects blocking calculations
+		if err := s.invalidateBlockedCache(ctx, conn); err != nil {
+			return fmt.Errorf("failed to invalidate blocked cache: %w", err)
+		}
 
-	if err := tx.Commit(); err != nil {
-		return wrapDBError("commit tombstone transaction", err)
-	}
-
-	return nil
+		return nil
+	})
 }
 
 // DeleteIssue permanently removes an issue from the database
@@ -1503,37 +1472,36 @@ func (s *SQLiteStorage) DeleteIssues(ctx context.Context, ids []string, cascade
 		return &DeleteIssuesResult{}, nil
 	}
 
-	tx, err := s.db.BeginTx(ctx, nil)
-	if err != nil {
-		return nil, fmt.Errorf("failed to begin transaction: %w", err)
-	}
-	defer func() { _ = tx.Rollback() }()
-
 	idSet := buildIDSet(ids)
 	result := &DeleteIssuesResult{}
 
-	expandedIDs, err := s.resolveDeleteSet(ctx, tx, ids, idSet, cascade, force, result)
+	// Execute in transaction using BEGIN IMMEDIATE (GH#1272 fix)
+	err := s.withTx(ctx, func(conn *sql.Conn) error {
+		expandedIDs, err := s.resolveDeleteSet(ctx, conn, ids, idSet, cascade, force, result)
+		if err != nil {
+			return wrapDBError("resolve delete set", err)
+		}
+
+		inClause, args := buildSQLInClause(expandedIDs)
+		if err := s.populateDeleteStats(ctx, conn, inClause, args, result); err != nil {
+			return err
+		}
+
+		if dryRun {
+			return nil
+		}
+
+		if err := s.executeDelete(ctx, conn, inClause, args, result); err != nil {
+			return err
+		}
+
+		return nil
+	})
+
 	if err != nil {
-		return nil, wrapDBError("resolve delete set", err)
-	}
-
-	inClause, args := buildSQLInClause(expandedIDs)
-	if err := s.populateDeleteStats(ctx, tx, inClause, args, result); err != nil {
 		return nil, err
 	}
 
-	if dryRun {
-		return result, nil
-	}
-
-	if err := s.executeDelete(ctx, tx, inClause, args, result); err != nil {
-		return nil, err
-	}
-
-	if err := tx.Commit(); err != nil {
-		return nil, fmt.Errorf("failed to commit transaction: %w", err)
-	}
-
 	// REMOVED: Counter sync after deletion - no longer needed with hash IDs
 
 	return result, nil
@@ -1547,18 +1515,18 @@ func buildIDSet(ids []string) map[string]bool {
 	return idSet
 }
 
-func (s *SQLiteStorage) resolveDeleteSet(ctx context.Context, tx *sql.Tx, ids []string, idSet map[string]bool, cascade bool, force bool, result *DeleteIssuesResult) ([]string, error) {
+func (s *SQLiteStorage) resolveDeleteSet(ctx context.Context, exec dbExecutor, ids []string, idSet map[string]bool, cascade bool, force bool, result *DeleteIssuesResult) ([]string, error) {
 	if cascade {
-		return s.expandWithDependents(ctx, tx, ids, idSet)
+		return s.expandWithDependents(ctx, exec, ids, idSet)
 	}
 	if !force {
-		return ids, s.validateNoDependents(ctx, tx, ids, idSet, result)
+		return ids, s.validateNoDependents(ctx, exec, ids, idSet, result)
 	}
-	return ids, s.trackOrphanedIssues(ctx, tx, ids, idSet, result)
+	return ids, s.trackOrphanedIssues(ctx, exec, ids, idSet, result)
 }
 
-func (s *SQLiteStorage) expandWithDependents(ctx context.Context, tx *sql.Tx, ids []string, _ map[string]bool) ([]string, error) {
-	allToDelete, err := s.findAllDependentsRecursive(ctx, tx, ids)
+func (s *SQLiteStorage) expandWithDependents(ctx context.Context, exec dbExecutor, ids []string, _ map[string]bool) ([]string, error) {
+	allToDelete, err := s.findAllDependentsRecursive(ctx, exec, ids)
 	if err != nil {
 		return nil, fmt.Errorf("failed to find dependents: %w", err)
 	}
@@ -1569,18 +1537,18 @@ func (s *SQLiteStorage) expandWithDependents(ctx context.Context, tx *sql.Tx, id
 	return expandedIDs, nil
 }
 
-func (s *SQLiteStorage) validateNoDependents(ctx context.Context, tx *sql.Tx, ids []string, idSet map[string]bool, result *DeleteIssuesResult) error {
+func (s *SQLiteStorage) validateNoDependents(ctx context.Context, exec dbExecutor, ids []string, idSet map[string]bool, result *DeleteIssuesResult) error {
 	for _, id := range ids {
-		if err := s.checkSingleIssueValidation(ctx, tx, id, idSet, result); err != nil {
+		if err := s.checkSingleIssueValidation(ctx, exec, id, idSet, result); err != nil {
 			return wrapDBError("check dependents", err)
 		}
 	}
 	return nil
 }
 
-func (s *SQLiteStorage) checkSingleIssueValidation(ctx context.Context, tx *sql.Tx, id string, idSet map[string]bool, result *DeleteIssuesResult) error {
+func (s *SQLiteStorage) checkSingleIssueValidation(ctx context.Context, exec dbExecutor, id string, idSet map[string]bool, result *DeleteIssuesResult) error {
 	var depCount int
-	err := tx.QueryRowContext(ctx,
+	err := exec.QueryRowContext(ctx,
 		`SELECT COUNT(*) FROM dependencies WHERE depends_on_id = ?`, id).Scan(&depCount)
 	if err != nil {
 		return fmt.Errorf("failed to check dependents for %s: %w", id, err)
@@ -1589,7 +1557,7 @@ func (s *SQLiteStorage) checkSingleIssueValidation(ctx context.Context, tx *sql.
 		return nil
 	}
 
-	rows, err := tx.QueryContext(ctx,
+	rows, err := exec.QueryContext(ctx,
 		`SELECT issue_id FROM dependencies WHERE depends_on_id = ?`, id)
 	if err != nil {
 		return fmt.Errorf("failed to get dependents for %s: %w", id, err)
@@ -1618,10 +1586,10 @@ func (s *SQLiteStorage) checkSingleIssueValidation(ctx context.Context, tx *sql.
 	return nil
 }
 
-func (s *SQLiteStorage) trackOrphanedIssues(ctx context.Context, tx *sql.Tx, ids []string, idSet map[string]bool, result *DeleteIssuesResult) error {
+func (s *SQLiteStorage) trackOrphanedIssues(ctx context.Context, exec dbExecutor, ids []string, idSet map[string]bool, result *DeleteIssuesResult) error {
 	orphanSet := make(map[string]bool)
 	for _, id := range ids {
-		if err := s.collectOrphansForID(ctx, tx, id, idSet, orphanSet); err != nil {
+		if err := s.collectOrphansForID(ctx, exec, id, idSet, orphanSet); err != nil {
 			return wrapDBError("collect orphans", err)
 		}
 	}
@@ -1631,8 +1599,8 @@ func (s *SQLiteStorage) trackOrphanedIssues(ctx context.Context, tx *sql.Tx, ids
 	return nil
 }
 
-func (s *SQLiteStorage) collectOrphansForID(ctx context.Context, tx *sql.Tx, id string, idSet map[string]bool, orphanSet map[string]bool) error {
-	rows, err := tx.QueryContext(ctx,
+func (s *SQLiteStorage) collectOrphansForID(ctx context.Context, exec dbExecutor, id string, idSet map[string]bool, orphanSet map[string]bool) error {
+	rows, err := exec.QueryContext(ctx,
 		`SELECT issue_id FROM dependencies WHERE depends_on_id = ?`, id)
 	if err != nil {
 		return fmt.Errorf("failed to get dependents for %s: %w", id, err)
@@ -1661,7 +1629,7 @@ func buildSQLInClause(ids []string) (string, []interface{}) {
 	return strings.Join(placeholders, ","), args
 }
 
-func (s *SQLiteStorage) populateDeleteStats(ctx context.Context, tx *sql.Tx, inClause string, args []interface{}, result *DeleteIssuesResult) error {
+func (s *SQLiteStorage) populateDeleteStats(ctx context.Context, exec dbExecutor, inClause string, args []interface{}, result *DeleteIssuesResult) error {
 	counts := []struct {
 		query string
 		dest  *int
@@ -1676,7 +1644,7 @@ func (s *SQLiteStorage) populateDeleteStats(ctx context.Context, tx *sql.Tx, inC
 		if c.dest == &result.DependenciesCount {
 			queryArgs = append(args, args...)
 		}
-		if err := tx.QueryRowContext(ctx, c.query, queryArgs...).Scan(c.dest); err != nil {
+		if err := exec.QueryRowContext(ctx, c.query, queryArgs...).Scan(c.dest); err != nil {
 			return fmt.Errorf("failed to count: %w", err)
 		}
 	}
@@ -1685,12 +1653,12 @@ func (s *SQLiteStorage) populateDeleteStats(ctx context.Context, tx *sql.Tx, inC
 	return nil
 }
 
-func (s *SQLiteStorage) executeDelete(ctx context.Context, tx *sql.Tx, inClause string, args []interface{}, result *DeleteIssuesResult) error {
+func (s *SQLiteStorage) executeDelete(ctx context.Context, exec dbExecutor, inClause string, args []interface{}, result *DeleteIssuesResult) error {
 	// Note: This method now creates tombstones instead of hard-deleting
 	// Only dependencies are deleted - issues are converted to tombstones
 
 	// 1. Delete dependencies - tombstones don't block other issues
-	_, err := tx.ExecContext(ctx,
+	_, err := exec.ExecContext(ctx,
 		fmt.Sprintf(`DELETE FROM dependencies WHERE issue_id IN (%s) OR depends_on_id IN (%s)`, inClause, inClause),
 		append(args, args...)...)
 	if err != nil {
@@ -1699,7 +1667,7 @@ func (s *SQLiteStorage) executeDelete(ctx context.Context, tx *sql.Tx, inClause
 
 	// 2. Get issue types before converting to tombstones (need for original_type)
 	issueTypes := make(map[string]string)
-	rows, err := tx.QueryContext(ctx,
+	rows, err := exec.QueryContext(ctx,
 		fmt.Sprintf(`SELECT id, issue_type FROM issues WHERE id IN (%s)`, inClause),
 		args...)
 	if err != nil {
@@ -1721,7 +1689,7 @@ func (s *SQLiteStorage) executeDelete(ctx context.Context, tx *sql.Tx, inClause
 	now := time.Now()
 	deletedCount := 0
 	for id, originalType := range issueTypes {
-		execResult, err := tx.ExecContext(ctx, `
+		execResult, err := exec.ExecContext(ctx, `
 			UPDATE issues
 			SET status = ?,
 			    closed_at = NULL,
@@ -1743,7 +1711,7 @@ func (s *SQLiteStorage) executeDelete(ctx context.Context, tx *sql.Tx, inClause
 		deletedCount++
 
 		// Record tombstone creation event
-		_, err = tx.ExecContext(ctx, `
+		_, err = exec.ExecContext(ctx, `
 			INSERT INTO events (issue_id, event_type, actor, comment)
 			VALUES (?, ?, ?, ?)
 		`, id, "deleted", "batch delete", "batch delete")
@@ -1752,7 +1720,7 @@ func (s *SQLiteStorage) executeDelete(ctx context.Context, tx *sql.Tx, inClause
 		}
 
 		// Mark issue as dirty for incremental export
-		_, err = tx.ExecContext(ctx, `
+		_, err = exec.ExecContext(ctx, `
 			INSERT INTO dirty_issues (issue_id, marked_at)
 			VALUES (?, ?)
 			ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
@@ -1763,7 +1731,7 @@ func (s *SQLiteStorage) executeDelete(ctx context.Context, tx *sql.Tx, inClause
 	}
 
 	// 4. Invalidate blocked issues cache since statuses changed
-	if err := s.invalidateBlockedCache(ctx, tx); err != nil {
+	if err := s.invalidateBlockedCache(ctx, exec); err != nil {
 		return fmt.Errorf("failed to invalidate blocked cache: %w", err)
 	}
 
@@ -1772,7 +1740,7 @@ func (s *SQLiteStorage) executeDelete(ctx context.Context, tx *sql.Tx, inClause
 }
 
 // findAllDependentsRecursive finds all issues that depend on the given issues, recursively
-func (s *SQLiteStorage) findAllDependentsRecursive(ctx context.Context, tx *sql.Tx, ids []string) (map[string]bool, error) {
+func (s *SQLiteStorage) findAllDependentsRecursive(ctx context.Context, exec dbExecutor, ids []string) (map[string]bool, error) {
 	result := make(map[string]bool)
 	for _, id := range ids {
 		result[id] = true
@@ -1785,7 +1753,7 @@ func (s *SQLiteStorage) findAllDependentsRecursive(ctx context.Context, tx *sql.
 		current := toProcess[0]
 		toProcess = toProcess[1:]
 
-		rows, err := tx.QueryContext(ctx,
+		rows, err := exec.QueryContext(ctx,
 			`SELECT issue_id FROM dependencies WHERE depends_on_id = ?`, current)
 		if err != nil {
 			return nil, err