Graph Construction & Validation

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build(repository: ParsedRepository): Graph {
    const graph: Graph = {
        nodes: new Map(),
        edges: new Map(),
        nodesByKind: new Map(),
        outgoingEdges: new Map(),
        incomingEdges: new Map(),
    };

    // Phase 1: Construct Nodes
    this.addFileNodes(graph, repository);
    this.addSymbolNodes(graph, repository);
    this.addDependencyNodes(graph, repository);
    this.addModuleNodes(graph, repository);

    // Phase 2: Construct & Index Edges
    this.addRelationshipEdges(graph, repository.relationships);

    // Phase 3 & 4: Dual Validation
    this.validateGraph(graph);    // Referential integrity (no dangling edges)
    this.validateIndexes(graph);  // Index consistency verification

    return graph;
}