feat(tombstone): add P2 code review improvements (bd-saa, bd-1bu, bd-nyt)

- Add partial index on deleted_at for efficient TTL queries
- Exclude tombstones from SearchIssues by default (new IncludeTombstones filter)
- Report tombstone count separately in GetStatistics
- Display tombstone count in bd stats output

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

internal/storage/sqlite/events.go

@@ -110,15 +110,16 @@ func (s *SQLiteStorage) GetEvents(ctx context.Context, issueID string, limit int
 func (s *SQLiteStorage) GetStatistics(ctx context.Context) (*types.Statistics, error) {
 	var stats types.Statistics
 
-	// Get counts
+	// Get counts (bd-nyt: exclude tombstones from TotalIssues, report separately)
 	err := s.db.QueryRowContext(ctx, `
 		SELECT
-			COUNT(*) as total,
+			COALESCE(SUM(CASE WHEN status != 'tombstone' THEN 1 ELSE 0 END), 0) as total,
 			COALESCE(SUM(CASE WHEN status = 'open' THEN 1 ELSE 0 END), 0) as open,
 			COALESCE(SUM(CASE WHEN status = 'in_progress' THEN 1 ELSE 0 END), 0) as in_progress,
-			COALESCE(SUM(CASE WHEN status = 'closed' THEN 1 ELSE 0 END), 0) as closed
+			COALESCE(SUM(CASE WHEN status = 'closed' THEN 1 ELSE 0 END), 0) as closed,
+			COALESCE(SUM(CASE WHEN status = 'tombstone' THEN 1 ELSE 0 END), 0) as tombstone
 		FROM issues
-	`).Scan(&stats.TotalIssues, &stats.OpenIssues, &stats.InProgressIssues, &stats.ClosedIssues)
+	`).Scan(&stats.TotalIssues, &stats.OpenIssues, &stats.InProgressIssues, &stats.ClosedIssues, &stats.TombstoneIssues)
 	if err != nil {
 		return nil, fmt.Errorf("failed to get issue counts: %w", err)
 	}

internal/storage/sqlite/migrations/018_tombstone_columns.go

@@ -43,5 +43,12 @@ func MigrateTombstoneColumns(db *sql.DB) error {
 		}
 	}
 
+	// Add partial index on deleted_at for efficient TTL queries (bd-saa)
+	// Only indexes non-NULL values, making it very efficient for tombstone filtering
+	_, err := db.Exec(`CREATE INDEX IF NOT EXISTS idx_issues_deleted_at ON issues(deleted_at) WHERE deleted_at IS NOT NULL`)
+	if err != nil {
+		return fmt.Errorf("failed to create deleted_at index: %w", err)
+	}
+
 	return nil
 }

internal/storage/sqlite/queries.go

@@ -1186,6 +1186,10 @@ func (s *SQLiteStorage) SearchIssues(ctx context.Context, query string, filter t
 	if filter.Status != nil {
 		whereClauses = append(whereClauses, "status = ?")
 		args = append(args, *filter.Status)
+	} else if !filter.IncludeTombstones {
+		// Exclude tombstones by default unless explicitly filtering for them (bd-1bu)
+		whereClauses = append(whereClauses, "status != ?")
+		args = append(args, types.StatusTombstone)
 	}
 
 	if filter.Priority != nil {

internal/storage/sqlite/transaction.go

@@ -919,6 +919,10 @@ func (t *sqliteTxStorage) SearchIssues(ctx context.Context, query string, filter
 	if filter.Status != nil {
 		whereClauses = append(whereClauses, "status = ?")
 		args = append(args, *filter.Status)
+	} else if !filter.IncludeTombstones {
+		// Exclude tombstones by default unless explicitly filtering for them (bd-1bu)
+		whereClauses = append(whereClauses, "status != ?")
+		args = append(args, types.StatusTombstone)
 	}
 
 	if filter.Priority != nil {