Cleanup and fixes: godoc comments, removed dead code, fixed renumber FK constraint bug

- Added comprehensive godoc comments for auto-flush functions (bd-4)
- Removed unused issueMap in scoreCollisions (bd-6)
- Fixed renumber command FK constraint failure (bd-143)
  - Changed UpdateIssueID to use explicit connection with FK disabled
  - Resolves 'constraint failed: FOREIGN KEY constraint failed' error
- Deleted 22 test/placeholder issues
- Renumbered issues from bd-1 to bd-143 (eliminated gaps)

Amp-Thread-ID: https://ampcode.com/threads/T-65f78f08-4856-4af0-9d6c-af33e88b5f63
Co-authored-by: Amp <amp@ampcode.com>

internal/storage/sqlite/sqlite.go

@@ -1149,18 +1149,25 @@ func (s *SQLiteStorage) UpdateIssue(ctx context.Context, id string, updates map[
 
 // UpdateIssueID updates an issue ID and all its text fields in a single transaction
 func (s *SQLiteStorage) UpdateIssueID(ctx context.Context, oldID, newID string, issue *types.Issue, actor string) error {
-	tx, err := s.db.BeginTx(ctx, nil)
+	// Get exclusive connection to ensure PRAGMA applies
+	conn, err := s.db.Conn(ctx)
+	if err != nil {
+		return fmt.Errorf("failed to get connection: %w", err)
+	}
+	defer conn.Close()
+
+	// Disable foreign keys on this specific connection
+	_, err = conn.ExecContext(ctx, `PRAGMA foreign_keys = OFF`)
+	if err != nil {
+		return fmt.Errorf("failed to disable foreign keys: %w", err)
+	}
+
+	tx, err := conn.BeginTx(ctx, nil)
 	if err != nil {
 		return fmt.Errorf("failed to begin transaction: %w", err)
 	}
 	defer tx.Rollback()
 
-	// Defer foreign key checks until end of transaction
-	_, err = tx.ExecContext(ctx, `PRAGMA defer_foreign_keys = ON`)
-	if err != nil {
-		return fmt.Errorf("failed to defer foreign keys: %w", err)
-	}
-
 	_, err = tx.ExecContext(ctx, `
 		UPDATE issues
 		SET id = ?, title = ?, description = ?, design = ?, acceptance_criteria = ?, notes = ?, updated_at = ?