Fix code review issues bd-19 through bd-23

- bd-19: Fix import zero-value field handling using JSON presence detection
- bd-20: Add --strict flag for dependency import failures
- bd-21: Simplify getNextID SQL query (reduce params from 4 to 2)
- bd-22: Add validation/warning for malformed issue IDs
- bd-23: Optimize export dependency queries (fix N+1 problem)

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

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

internal/storage/sqlite/dependencies.go

@@ -210,6 +210,39 @@ func (s *SQLiteStorage) GetDependencyRecords(ctx context.Context, issueID string
 	return deps, nil
 }
 
+// GetAllDependencyRecords returns all dependency records grouped by issue ID
+// This is optimized for bulk export operations to avoid N+1 queries
+func (s *SQLiteStorage) GetAllDependencyRecords(ctx context.Context) (map[string][]*types.Dependency, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT issue_id, depends_on_id, type, created_at, created_by
+		FROM dependencies
+		ORDER BY issue_id, created_at ASC
+	`)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get all dependency records: %w", err)
+	}
+	defer rows.Close()
+
+	// Group dependencies by issue ID
+	depsMap := make(map[string][]*types.Dependency)
+	for rows.Next() {
+		var dep types.Dependency
+		err := rows.Scan(
+			&dep.IssueID,
+			&dep.DependsOnID,
+			&dep.Type,
+			&dep.CreatedAt,
+			&dep.CreatedBy,
+		)
+		if err != nil {
+			return nil, fmt.Errorf("failed to scan dependency: %w", err)
+		}
+		depsMap[dep.IssueID] = append(depsMap[dep.IssueID], &dep)
+	}
+
+	return depsMap, nil
+}
+
 // GetDependencyTree returns the full dependency tree
 func (s *SQLiteStorage) GetDependencyTree(ctx context.Context, issueID string, maxDepth int) ([]*types.TreeNode, error) {
 	if maxDepth <= 0 {

internal/storage/sqlite/sqlite.go

@@ -74,13 +74,36 @@ func getNextID(db *sql.DB) int {
 		SELECT MAX(CAST(SUBSTR(id, LENGTH(?) + 2) AS INTEGER))
 		FROM issues
 		WHERE id LIKE ? || '-%'
-		AND SUBSTR(id, 1, LENGTH(?)) = ?
 	`
-	err = db.QueryRow(query, prefix, prefix, prefix, prefix).Scan(&maxNum)
+	err = db.QueryRow(query, prefix, prefix).Scan(&maxNum)
 	if err != nil || !maxNum.Valid {
 		return 1 // Start from 1 if table is empty or no matching IDs
 	}
 
+	// Check for malformed IDs (non-numeric suffixes) and warn
+	// These are silently ignored by CAST but indicate data quality issues
+	malformedQuery := `
+		SELECT id FROM issues
+		WHERE id LIKE ? || '-%'
+		AND CAST(SUBSTR(id, LENGTH(?) + 2) AS INTEGER) IS NULL
+	`
+	rows, err := db.Query(malformedQuery, prefix, prefix)
+	if err == nil {
+		defer rows.Close()
+		var malformedIDs []string
+		for rows.Next() {
+			var id string
+			if err := rows.Scan(&id); err == nil {
+				malformedIDs = append(malformedIDs, id)
+			}
+		}
+		if len(malformedIDs) > 0 {
+			fmt.Fprintf(os.Stderr, "Warning: Found %d malformed issue IDs with non-numeric suffixes: %v\n",
+				len(malformedIDs), malformedIDs)
+			fmt.Fprintf(os.Stderr, "These IDs are being ignored for ID generation. Consider fixing them.\n")
+		}
+	}
+
 	return int(maxNum.Int64) + 1
 }