@agentic-qe/v3 3.0.0-alpha.5 → 3.0.0-alpha.7

package/src/domains/code-intelligence/services/knowledge-graph.ts

@@ -1,1067 +0,0 @@
-/**
- * Agentic QE v3 - Knowledge Graph Service
- * Builds and queries knowledge graph for code relationships
- */
-
-import { Result, ok, err } from '../../../shared/types';
-import { TypeScriptParser } from '../../../shared/parsers';
-import { FileReader } from '../../../shared/io';
-import { NomicEmbedder } from '../../../shared/embeddings';
-import { MemoryBackend } from '../../../kernel/interfaces';
-import {
-  IndexRequest,
-  IndexResult,
-  IndexError,
-  KGQueryRequest,
-  KGQueryResult,
-  KGNode,
-  KGEdge,
-  DependencyRequest,
-  DependencyMap,
-  DependencyNode,
-  DependencyEdge,
-  DependencyMetrics,
-} from '../interfaces';
-
-/**
- * Interface for the knowledge graph service
- */
-export interface IKnowledgeGraphService {
-  /** Index files into the knowledge graph */
-  index(request: IndexRequest): Promise<Result<IndexResult, Error>>;
-
-  /** Query the knowledge graph */
-  query(request: KGQueryRequest): Promise<Result<KGQueryResult, Error>>;
-
-  /** Map dependencies for files */
-  mapDependencies(request: DependencyRequest): Promise<Result<DependencyMap, Error>>;
-
-  /** Get a node by ID */
-  getNode(nodeId: string): Promise<KGNode | undefined>;
-
-  /** Get edges for a node */
-  getEdges(nodeId: string, direction: 'incoming' | 'outgoing' | 'both'): Promise<KGEdge[]>;
-
-  /** Clear the knowledge graph */
-  clear(): Promise<void>;
-}
-
-/**
- * Configuration for the knowledge graph service
- */
-export interface KnowledgeGraphConfig {
-  maxNodes: number;
-  maxEdgesPerNode: number;
-  namespace: string;
-  enableVectorEmbeddings: boolean;
-  embeddingDimension: number;
-}
-
-const DEFAULT_CONFIG: KnowledgeGraphConfig = {
-  maxNodes: 100000,
-  maxEdgesPerNode: 500,
-  namespace: 'code-intelligence:kg',
-  enableVectorEmbeddings: true,
-  embeddingDimension: 384,
-};
-
-/**
- * Knowledge Graph Service Implementation
- * Builds and manages the code knowledge graph with relationships
- */
-export class KnowledgeGraphService implements IKnowledgeGraphService {
-  private readonly config: KnowledgeGraphConfig;
-  private readonly nodeCache: Map<string, KGNode> = new Map();
-  private readonly edgeIndex: Map<string, KGEdge[]> = new Map();
-  private readonly tsParser: TypeScriptParser;
-  private readonly fileReader: FileReader;
-  private readonly embedder: NomicEmbedder;
-
-  constructor(
-    private readonly memory: MemoryBackend,
-    config: Partial<KnowledgeGraphConfig> = {}
-  ) {
-    this.config = { ...DEFAULT_CONFIG, ...config };
-    this.tsParser = new TypeScriptParser();
-    this.fileReader = new FileReader();
-    this.embedder = new NomicEmbedder({
-      enableFallback: true,
-    });
-  }
-
-  /**
-   * Index files into the knowledge graph
-   */
-  async index(request: IndexRequest): Promise<Result<IndexResult, Error>> {
-    const startTime = Date.now();
-    const errors: IndexError[] = [];
-    let nodesCreated = 0;
-    let edgesCreated = 0;
-
-    try {
-      const { paths, incremental = false, includeTests = true, languages } = request;
-
-      // Clear existing graph if not incremental
-      if (!incremental) {
-        await this.clear();
-      }
-
-      for (const path of paths) {
-        try {
-          // Filter by language if specified
-          if (languages && languages.length > 0) {
-            const ext = this.getFileExtension(path);
-            if (!this.matchesLanguage(ext, languages)) {
-              continue;
-            }
-          }
-
-          // Skip test files if not included
-          if (!includeTests && this.isTestFile(path)) {
-            continue;
-          }
-
-          // Index the file
-          const result = await this.indexFile(path);
-          nodesCreated += result.nodes;
-          edgesCreated += result.edges;
-        } catch (fileError) {
-          errors.push({
-            file: path,
-            error: fileError instanceof Error ? fileError.message : String(fileError),
-          });
-        }
-      }
-
-      const duration = Date.now() - startTime;
-
-      // Store indexing metadata
-      await this.storeIndexMetadata({
-        filesIndexed: paths.length - errors.length,
-        nodesCreated,
-        edgesCreated,
-        duration,
-        indexedAt: new Date().toISOString(),
-      });
-
-      return ok({
-        filesIndexed: paths.length - errors.length,
-        nodesCreated,
-        edgesCreated,
-        duration,
-        errors,
-      });
-    } catch (error) {
-      return err(error instanceof Error ? error : new Error(String(error)));
-    }
-  }
-
-  /**
-   * Query the knowledge graph
-   */
-  async query(request: KGQueryRequest): Promise<Result<KGQueryResult, Error>> {
-    try {
-      const { query: queryStr, type, limit = 100 } = request;
-
-      if (type === 'cypher') {
-        return this.executeCypherQuery(queryStr, limit);
-      } else {
-        return this.executeNaturalLanguageQuery(queryStr, limit);
-      }
-    } catch (error) {
-      return err(error instanceof Error ? error : new Error(String(error)));
-    }
-  }
-
-  /**
-   * Map dependencies for given files
-   */
-  async mapDependencies(request: DependencyRequest): Promise<Result<DependencyMap, Error>> {
-    try {
-      const { files, direction, depth = 3 } = request;
-      const nodes: DependencyNode[] = [];
-      const edges: DependencyEdge[] = [];
-      const visited = new Set<string>();
-      const cycles: string[][] = [];
-
-      // Process each file
-      for (const file of files) {
-        await this.traverseDependencies(
-          file,
-          direction,
-          depth,
-          visited,
-          nodes,
-          edges,
-          [],
-          cycles
-        );
-      }
-
-      // Calculate metrics
-      const metrics = this.calculateDependencyMetrics(nodes, edges);
-
-      return ok({
-        nodes,
-        edges,
-        cycles,
-        metrics,
-      });
-    } catch (error) {
-      return err(error instanceof Error ? error : new Error(String(error)));
-    }
-  }
-
-  /**
-   * Get a node by ID
-   */
-  async getNode(nodeId: string): Promise<KGNode | undefined> {
-    // Check cache first
-    if (this.nodeCache.has(nodeId)) {
-      return this.nodeCache.get(nodeId);
-    }
-
-    // Load from memory
-    const key = `${this.config.namespace}:node:${nodeId}`;
-    const node = await this.memory.get<KGNode>(key);
-
-    if (node) {
-      this.nodeCache.set(nodeId, node);
-    }
-
-    return node;
-  }
-
-  /**
-   * Get edges for a node
-   */
-  async getEdges(
-    nodeId: string,
-    direction: 'incoming' | 'outgoing' | 'both'
-  ): Promise<KGEdge[]> {
-    const edges: KGEdge[] = [];
-
-    // Check index first
-    const cachedEdges = this.edgeIndex.get(nodeId);
-    if (cachedEdges) {
-      return this.filterEdgesByDirection(cachedEdges, nodeId, direction);
-    }
-
-    // Load from memory
-    const pattern = `${this.config.namespace}:edge:*`;
-    const keys = await this.memory.search(pattern, this.config.maxEdgesPerNode * 2);
-
-    for (const key of keys) {
-      const edge = await this.memory.get<KGEdge>(key);
-      if (edge) {
-        const matches =
-          (direction !== 'outgoing' && edge.target === nodeId) ||
-          (direction !== 'incoming' && edge.source === nodeId);
-
-        if (matches) {
-          edges.push(edge);
-        }
-      }
-    }
-
-    return edges;
-  }
-
-  /**
-   * Clear the knowledge graph
-   */
-  async clear(): Promise<void> {
-    // Clear caches
-    this.nodeCache.clear();
-    this.edgeIndex.clear();
-
-    // Clear persisted data
-    const nodePattern = `${this.config.namespace}:node:*`;
-    const edgePattern = `${this.config.namespace}:edge:*`;
-
-    const nodeKeys = await this.memory.search(nodePattern, this.config.maxNodes);
-    const edgeKeys = await this.memory.search(edgePattern, this.config.maxNodes * 10);
-
-    for (const key of [...nodeKeys, ...edgeKeys]) {
-      await this.memory.delete(key);
-    }
-  }
-
-  // ============================================================================
-  // Private Helper Methods
-  // ============================================================================
-
-  private async indexFile(
-    filePath: string
-  ): Promise<{ nodes: number; edges: number }> {
-    let nodesCreated = 0;
-    let edgesCreated = 0;
-
-    // Create file node
-    const fileNode = await this.createFileNode(filePath);
-    nodesCreated++;
-
-    // Parse file to extract entities using TypeScript AST parser
-    const entities = await this.extractEntities(filePath);
-
-    for (const entity of entities) {
-      // Create entity node
-      const entityNode = await this.createEntityNode(entity, filePath);
-      nodesCreated++;
-
-      // Create edge from file to entity
-      await this.createEdge(fileNode.id, entityNode.id, 'contains');
-      edgesCreated++;
-    }
-
-    // Extract imports/dependencies
-    const imports = await this.extractImports(filePath);
-
-    for (const importPath of imports) {
-      // Create dependency edge
-      const targetNodeId = this.pathToNodeId(importPath);
-      await this.createEdge(fileNode.id, targetNodeId, 'import');
-      edgesCreated++;
-    }
-
-    return { nodes: nodesCreated, edges: edgesCreated };
-  }
-
-  private async createFileNode(filePath: string): Promise<KGNode> {
-    const nodeId = this.pathToNodeId(filePath);
-    const node: KGNode = {
-      id: nodeId,
-      label: 'File',
-      properties: {
-        path: filePath,
-        name: this.getFileName(filePath),
-        extension: this.getFileExtension(filePath),
-        type: this.getFileType(filePath),
-      },
-    };
-
-    await this.storeNode(node);
-    return node;
-  }
-
-  private async createEntityNode(
-    entity: ExtractedEntity,
-    filePath: string
-  ): Promise<KGNode> {
-    const nodeId = `${this.pathToNodeId(filePath)}:${entity.type}:${entity.name}`;
-    const node: KGNode = {
-      id: nodeId,
-      label: entity.type,
-      properties: {
-        name: entity.name,
-        file: filePath,
-        line: entity.line,
-        visibility: entity.visibility,
-        async: entity.isAsync,
-      },
-    };
-
-    await this.storeNode(node);
-
-    // Store vector embedding for semantic search
-    if (this.config.enableVectorEmbeddings) {
-      const embedding = await this.generateEmbedding(entity);
-      await this.memory.storeVector(`${this.config.namespace}:node:${nodeId}`, embedding, {
-        nodeId,
-        type: entity.type,
-        name: entity.name,
-      });
-    }
-
-    return node;
-  }
-
-  private async createEdge(
-    sourceId: string,
-    targetId: string,
-    type: DependencyEdge['type'] | 'contains'
-  ): Promise<KGEdge> {
-    const edgeId = `${sourceId}--${type}-->${targetId}`;
-    const edge: KGEdge = {
-      source: sourceId,
-      target: targetId,
-      type,
-    };
-
-    // Store edge
-    await this.memory.set(`${this.config.namespace}:edge:${edgeId}`, edge, {
-      namespace: this.config.namespace,
-    });
-
-    // Update edge index
-    const sourceEdges = this.edgeIndex.get(sourceId) || [];
-    sourceEdges.push(edge);
-    this.edgeIndex.set(sourceId, sourceEdges);
-
-    return edge;
-  }
-
-  private async storeNode(node: KGNode): Promise<void> {
-    await this.memory.set(`${this.config.namespace}:node:${node.id}`, node, {
-      namespace: this.config.namespace,
-    });
-    this.nodeCache.set(node.id, node);
-  }
-
-  private async extractEntities(filePath: string): Promise<ExtractedEntity[]> {
-    const extension = this.getFileExtension(filePath);
-    const entities: ExtractedEntity[] = [];
-
-    // Use TypeScript parser for TS/JS files
-    if (['ts', 'tsx', 'js', 'jsx'].includes(extension)) {
-      const fileResult = await this.fileReader.readFile(filePath);
-
-      if (fileResult.success) {
-        const fileName = this.getFileName(filePath);
-        const ast = this.tsParser.parseFile(fileName, fileResult.value);
-
-        // Extract functions
-        const functions = this.tsParser.extractFunctions(ast);
-        for (const func of functions) {
-          entities.push({
-            type: 'function',
-            name: func.name,
-            line: func.startLine,
-            visibility: 'public',
-            isAsync: func.isAsync,
-          });
-        }
-
-        // Extract classes
-        const classes = this.tsParser.extractClasses(ast);
-        for (const cls of classes) {
-          entities.push({
-            type: 'class',
-            name: cls.name,
-            line: cls.startLine,
-            visibility: 'public',
-            isAsync: false,
-          });
-
-          // Add class methods as entities
-          for (const method of cls.methods) {
-            entities.push({
-              type: 'function',
-              name: `${cls.name}.${method.name}`,
-              line: method.startLine,
-              visibility: method.visibility,
-              isAsync: method.isAsync,
-            });
-          }
-        }
-
-        // Extract interfaces
-        const interfaces = this.tsParser.extractInterfaces(ast);
-        for (const iface of interfaces) {
-          entities.push({
-            type: 'interface',
-            name: iface.name,
-            line: iface.startLine,
-            visibility: 'public',
-            isAsync: false,
-          });
-        }
-
-        // If no entities found, create a module entity for the file
-        if (entities.length === 0) {
-          entities.push({
-            type: 'module',
-            name: fileName.replace(/\.[^.]+$/, ''),
-            line: 1,
-            visibility: 'public',
-            isAsync: false,
-          });
-        }
-      } else {
-        // Fallback: create a module entity for the file itself
-        entities.push({
-          type: 'module',
-          name: this.getFileName(filePath).replace(/\.[^.]+$/, ''),
-          line: 1,
-          visibility: 'public',
-          isAsync: false,
-        });
-      }
-    } else if (extension === 'py') {
-      // Python files: regex-based parsing for classes, functions, imports
-      const fileResult = await this.fileReader.readFile(filePath);
-
-      if (fileResult.success) {
-        const content = fileResult.value;
-        const lines = content.split('\n');
-
-        // Extract class definitions: class ClassName(Base): or class ClassName:
-        const classPattern = /^class\s+(\w+)\s*(?:\([^)]*\))?\s*:/;
-        // Extract function definitions: def function_name(...): or async def function_name(...):
-        const funcPattern = /^(async\s+)?def\s+(\w+)\s*\(/;
-
-        let currentClass: string | null = null;
-        let currentIndent = 0;
-
-        for (let i = 0; i < lines.length; i++) {
-          const line = lines[i];
-          const lineNum = i + 1;
-          const trimmedLine = line.trimStart();
-          const indent = line.length - trimmedLine.length;
-
-          // Track class scope for methods
-          if (currentClass && indent <= currentIndent) {
-            currentClass = null;
-          }
-
-          // Match class definitions
-          const classMatch = trimmedLine.match(classPattern);
-          if (classMatch) {
-            const className = classMatch[1];
-            entities.push({
-              type: 'class',
-              name: className,
-              line: lineNum,
-              visibility: className.startsWith('_') ? 'private' : 'public',
-              isAsync: false,
-            });
-            currentClass = className;
-            currentIndent = indent;
-            continue;
-          }
-
-          // Match function/method definitions
-          const funcMatch = trimmedLine.match(funcPattern);
-          if (funcMatch) {
-            const isAsync = !!funcMatch[1];
-            const funcName = funcMatch[2];
-            const isMethod = currentClass !== null && indent > currentIndent;
-
-            // Determine visibility
-            let visibility: 'public' | 'private' | 'protected' = 'public';
-            if (funcName.startsWith('__') && !funcName.endsWith('__')) {
-              visibility = 'private'; // Name-mangled private
-            } else if (funcName.startsWith('_')) {
-              visibility = 'protected'; // Convention private
-            }
-
-            entities.push({
-              type: 'function',
-              name: isMethod ? `${currentClass}.${funcName}` : funcName,
-              line: lineNum,
-              visibility,
-              isAsync,
-            });
-          }
-        }
-
-        // If no entities found, create a module entity for the file
-        if (entities.length === 0) {
-          entities.push({
-            type: 'module',
-            name: this.getFileName(filePath).replace('.py', ''),
-            line: 1,
-            visibility: 'public',
-            isAsync: false,
-          });
-        }
-      } else {
-        // Fallback: create a module entity for the file itself
-        entities.push({
-          type: 'module',
-          name: this.getFileName(filePath).replace('.py', ''),
-          line: 1,
-          visibility: 'public',
-          isAsync: false,
-        });
-      }
-    }
-
-    return entities;
-  }
-
-  private async extractImports(filePath: string): Promise<string[]> {
-    const extension = this.getFileExtension(filePath);
-    const importPaths: string[] = [];
-
-    // Use TypeScript parser for TS/JS files
-    if (['ts', 'tsx', 'js', 'jsx'].includes(extension)) {
-      const fileResult = await this.fileReader.readFile(filePath);
-
-      if (fileResult.success) {
-        const fileName = this.getFileName(filePath);
-        const ast = this.tsParser.parseFile(fileName, fileResult.value);
-        const imports = this.tsParser.extractImports(ast);
-
-        // Extract import sources (module property in new API)
-        for (const importInfo of imports) {
-          // Only include relative imports and package imports
-          // Skip node built-ins for now
-          if (!importInfo.module.startsWith('node:')) {
-            importPaths.push(importInfo.module);
-          }
-        }
-      }
-    }
-
-    return importPaths;
-  }
-
-  private async executeCypherQuery(
-    query: string,
-    limit: number
-  ): Promise<Result<KGQueryResult, Error>> {
-    // Cypher query parser supporting:
-    // - MATCH (n:Label) - node patterns
-    // - MATCH (n:Label)-[r:REL_TYPE]->(m:Label) - relationship patterns
-    // - WHERE n.property = 'value' - property filters
-    // - RETURN n, r, m - result selection (implicit: all matched)
-
-    const nodes: KGNode[] = [];
-    const edges: KGEdge[] = [];
-    const nodeAliases: Map<string, KGNode[]> = new Map();
-
-    // Parse relationship pattern: MATCH (a:Label1)-[r:RelType]->(b:Label2)
-    const relationshipPattern =
-      /MATCH\s+\((\w+):(\w+)\)\s*-\[(\w+)?:?(\w+)?\]\s*->\s*\((\w+):(\w+)\)/i.exec(query);
-
-    if (relationshipPattern) {
-      const [, sourceAlias, sourceLabel, , relType, targetAlias, targetLabel] =
-        relationshipPattern;
-
-      // Find source nodes
-      const sourceNodes = await this.findNodesByLabel(sourceLabel, limit * 2);
-      nodeAliases.set(sourceAlias, sourceNodes);
-
-      // For each source node, find relationships and target nodes
-      for (const sourceNode of sourceNodes.slice(0, limit)) {
-        const nodeEdges = await this.getEdges(sourceNode.id, 'outgoing');
-
-        for (const edge of nodeEdges) {
-          // Filter by relationship type if specified
-          if (relType && edge.type !== relType) continue;
-
-          const targetNode = await this.getNode(edge.target);
-          if (targetNode && targetNode.label === targetLabel) {
-            if (!nodes.some((n) => n.id === sourceNode.id)) {
-              nodes.push(sourceNode);
-            }
-            if (!nodes.some((n) => n.id === targetNode.id)) {
-              nodes.push(targetNode);
-            }
-            // Use source+target+type as unique edge identifier
-            if (!edges.some((e) => e.source === edge.source && e.target === edge.target && e.type === edge.type)) {
-              edges.push(edge);
-            }
-          }
-        }
-      }
-
-      if (targetAlias) {
-        nodeAliases.set(
-          targetAlias,
-          nodes.filter((n) => n.label === targetLabel)
-        );
-      }
-    } else {
-      // Parse simple node pattern: MATCH (n:Label)
-      const matchPattern = /MATCH\s+\((\w+):(\w+)\)/i.exec(query);
-      if (matchPattern) {
-        const [, alias, label] = matchPattern;
-        const matchedNodes = await this.findNodesByLabel(label, limit);
-        nodeAliases.set(alias, matchedNodes);
-        nodes.push(...matchedNodes);
-      }
-    }
-
-    // Parse WHERE clause for property filtering
-    const wherePattern = /WHERE\s+(\w+)\.(\w+)\s*=\s*['"]?([^'")\s]+)['"]?/i.exec(query);
-    if (wherePattern) {
-      const [, alias, property, value] = wherePattern;
-      const aliasNodes = nodeAliases.get(alias) || nodes;
-
-      // Filter nodes by property value
-      const filteredNodes = aliasNodes.filter((node) => {
-        const propValue = node.properties[property];
-        return propValue !== undefined && String(propValue) === value;
-      });
-
-      // Replace nodes with filtered set
-      nodes.length = 0;
-      nodes.push(...filteredNodes.slice(0, limit));
-
-      // Also filter edges to only include those connecting filtered nodes
-      const nodeIds = new Set(nodes.map((n) => n.id));
-      const filteredEdges = edges.filter(
-        (e) => nodeIds.has(e.source) && nodeIds.has(e.target)
-      );
-      edges.length = 0;
-      edges.push(...filteredEdges);
-    }
-
-    return ok({
-      nodes: nodes.slice(0, limit),
-      edges,
-      metadata: {
-        query,
-        type: 'cypher',
-        resultCount: nodes.length,
-        edgeCount: edges.length,
-      },
-    });
-  }
-
-  /**
-   * Find nodes by their label
-   */
-  private async findNodesByLabel(label: string, limit: number): Promise<KGNode[]> {
-    const nodes: KGNode[] = [];
-    const pattern = `${this.config.namespace}:node:*`;
-    const keys = await this.memory.search(pattern, limit * 2);
-
-    for (const key of keys) {
-      const node = await this.memory.get<KGNode>(key);
-      if (node && node.label === label) {
-        nodes.push(node);
-        if (nodes.length >= limit) break;
-      }
-    }
-
-    return nodes;
-  }
-
-  private async executeNaturalLanguageQuery(
-    query: string,
-    limit: number
-  ): Promise<Result<KGQueryResult, Error>> {
-    // Use vector search for natural language queries
-    if (this.config.enableVectorEmbeddings) {
-      const queryEmbedding = await this.generateQueryEmbedding(query);
-      const results = await this.memory.vectorSearch(queryEmbedding, limit);
-
-      const nodes: KGNode[] = [];
-      for (const result of results) {
-        const nodeId = (result.metadata as { nodeId: string })?.nodeId;
-        if (nodeId) {
-          const node = await this.getNode(nodeId);
-          if (node) {
-            nodes.push(node);
-          }
-        }
-      }
-
-      return ok({
-        nodes,
-        edges: [],
-        metadata: {
-          query,
-          type: 'natural-language',
-          resultCount: nodes.length,
-          searchScores: results.map((r) => r.score),
-        },
-      });
-    }
-
-    // Fallback to keyword matching
-    const keywords = query.toLowerCase().split(/\s+/);
-    const pattern = `${this.config.namespace}:node:*`;
-    const keys = await this.memory.search(pattern, limit * 3);
-
-    const nodes: KGNode[] = [];
-    for (const key of keys) {
-      const node = await this.memory.get<KGNode>(key);
-      if (node) {
-        const nodeText = JSON.stringify(node.properties).toLowerCase();
-        if (keywords.some((kw) => nodeText.includes(kw))) {
-          nodes.push(node);
-          if (nodes.length >= limit) break;
-        }
-      }
-    }
-
-    return ok({
-      nodes,
-      edges: [],
-      metadata: {
-        query,
-        type: 'keyword',
-        resultCount: nodes.length,
-      },
-    });
-  }
-
-  private async traverseDependencies(
-    file: string,
-    direction: 'incoming' | 'outgoing' | 'both',
-    depth: number,
-    visited: Set<string>,
-    nodes: DependencyNode[],
-    edges: DependencyEdge[],
-    path: string[],
-    cycles: string[][]
-  ): Promise<void> {
-    if (depth <= 0 || visited.has(file)) {
-      // Check for cycle
-      const cycleStart = path.indexOf(file);
-      if (cycleStart >= 0) {
-        cycles.push([...path.slice(cycleStart), file]);
-      }
-      return;
-    }
-
-    visited.add(file);
-    path.push(file);
-
-    const nodeId = this.pathToNodeId(file);
-    const fileEdges = await this.getEdges(nodeId, direction);
-
-    // Create dependency node
-    const inDegree = fileEdges.filter((e) => e.target === nodeId).length;
-    const outDegree = fileEdges.filter((e) => e.source === nodeId).length;
-
-    nodes.push({
-      id: nodeId,
-      path: file,
-      type: 'file',
-      inDegree,
-      outDegree,
-    });
-
-    // Process edges
-    for (const edge of fileEdges) {
-      const depEdge: DependencyEdge = {
-        source: edge.source,
-        target: edge.target,
-        type: edge.type as DependencyEdge['type'],
-      };
-
-      if (!edges.some((e) => e.source === depEdge.source && e.target === depEdge.target)) {
-        edges.push(depEdge);
-      }
-
-      // Recursively traverse
-      const nextFile =
-        edge.source === nodeId
-          ? this.nodeIdToPath(edge.target)
-          : this.nodeIdToPath(edge.source);
-
-      if (nextFile) {
-        await this.traverseDependencies(
-          nextFile,
-          direction,
-          depth - 1,
-          visited,
-          nodes,
-          edges,
-          path,
-          cycles
-        );
-      }
-    }
-
-    path.pop();
-  }
-
-  private calculateDependencyMetrics(
-    nodes: DependencyNode[],
-    edges: DependencyEdge[]
-  ): DependencyMetrics {
-    const totalNodes = nodes.length;
-    const totalEdges = edges.length;
-    const avgDegree =
-      totalNodes > 0
-        ? nodes.reduce((sum, n) => sum + n.inDegree + n.outDegree, 0) / totalNodes
-        : 0;
-
-    // Calculate max depth using BFS
-    let maxDepth = 0;
-    if (nodes.length > 0) {
-      const adjList = new Map<string, string[]>();
-      for (const edge of edges) {
-        const sources = adjList.get(edge.source) || [];
-        sources.push(edge.target);
-        adjList.set(edge.source, sources);
-      }
-
-      const depths = new Map<string, number>();
-      for (const node of nodes) {
-        if (!depths.has(node.id)) {
-          this.bfsDepth(node.id, adjList, depths);
-        }
-        maxDepth = Math.max(maxDepth, depths.get(node.id) || 0);
-      }
-    }
-
-    // Simple cyclomatic complexity estimate
-    const cyclomaticComplexity = totalEdges - totalNodes + 2;
-
-    return {
-      totalNodes,
-      totalEdges,
-      avgDegree: Math.round(avgDegree * 100) / 100,
-      maxDepth,
-      cyclomaticComplexity: Math.max(1, cyclomaticComplexity),
-    };
-  }
-
-  private bfsDepth(
-    startId: string,
-    adjList: Map<string, string[]>,
-    depths: Map<string, number>
-  ): void {
-    const queue: Array<{ id: string; depth: number }> = [{ id: startId, depth: 0 }];
-
-    while (queue.length > 0) {
-      const current = queue.shift()!;
-      const existingDepth = depths.get(current.id) ?? -1;
-
-      if (current.depth > existingDepth) {
-        depths.set(current.id, current.depth);
-      }
-
-      const neighbors = adjList.get(current.id) || [];
-      for (const neighbor of neighbors) {
-        if (!depths.has(neighbor) || (depths.get(neighbor) ?? 0) < current.depth + 1) {
-          queue.push({ id: neighbor, depth: current.depth + 1 });
-        }
-      }
-    }
-  }
-
-  private filterEdgesByDirection(
-    edges: KGEdge[],
-    nodeId: string,
-    direction: 'incoming' | 'outgoing' | 'both'
-  ): KGEdge[] {
-    return edges.filter((edge) => {
-      if (direction === 'incoming') return edge.target === nodeId;
-      if (direction === 'outgoing') return edge.source === nodeId;
-      return true;
-    });
-  }
-
-  private async storeIndexMetadata(metadata: Record<string, unknown>): Promise<void> {
-    await this.memory.set(`${this.config.namespace}:metadata:index`, metadata, {
-      namespace: this.config.namespace,
-      persist: true,
-    });
-  }
-
-  private async generateEmbedding(entity: ExtractedEntity): Promise<number[]> {
-    // Create rich text representation of the entity for semantic embedding
-    const text = `${entity.type} ${entity.name} ${entity.visibility}${entity.isAsync ? ' async' : ''}`;
-
-    try {
-      // Use NomicEmbedder for real semantic embeddings (returns number[] directly)
-      const embedding = await this.embedder.embed(text);
-      return embedding;
-    } catch {
-      // Fall back to simple embedding if Ollama is unavailable
-      return this.fallbackEmbedding(text);
-    }
-  }
-
-  private async generateQueryEmbedding(query: string): Promise<number[]> {
-    try {
-      // Use NomicEmbedder for real semantic embeddings (returns number[] directly)
-      const embedding = await this.embedder.embed(query);
-      return embedding;
-    } catch {
-      // Fall back to simple embedding if Ollama is unavailable
-      return this.fallbackEmbedding(query);
-    }
-  }
-
-  private fallbackEmbedding(text: string): number[] {
-    // Fallback pseudo-embedding when Ollama is unavailable
-    const embedding = new Array(this.config.embeddingDimension).fill(0);
-    const words = text.toLowerCase().split(/\s+/);
-
-    for (let i = 0; i < words.length; i++) {
-      const word = words[i];
-      for (let j = 0; j < word.length && j < embedding.length; j++) {
-        embedding[(i + j) % embedding.length] += word.charCodeAt(j) / 1000;
-      }
-    }
-
-    const magnitude = Math.sqrt(embedding.reduce((sum, v) => sum + v * v, 0)) || 1;
-    return embedding.map((v) => v / magnitude);
-  }
-
-  private pathToNodeId(path: string): string {
-    return path.replace(/[/\\]/g, ':').replace(/\./g, '_');
-  }
-
-  private nodeIdToPath(nodeId: string): string | null {
-    // Reverse the nodeId transformation
-    const path = nodeId.replace(/:/g, '/').replace(/_(?=[^_]*$)/, '.');
-    return path.includes('/') ? path : null;
-  }
-
-  private getFileName(path: string): string {
-    return path.split(/[/\\]/).pop() || path;
-  }
-
-  private getFileExtension(path: string): string {
-    const name = this.getFileName(path);
-    const parts = name.split('.');
-    return parts.length > 1 ? parts.pop()! : '';
-  }
-
-  private getFileType(path: string): string {
-    const ext = this.getFileExtension(path);
-    const typeMap: Record<string, string> = {
-      ts: 'typescript',
-      tsx: 'typescript-react',
-      js: 'javascript',
-      jsx: 'javascript-react',
-      py: 'python',
-      go: 'go',
-      java: 'java',
-      rs: 'rust',
-      rb: 'ruby',
-      cs: 'csharp',
-    };
-    return typeMap[ext] || 'unknown';
-  }
-
-  private matchesLanguage(ext: string, languages: string[]): boolean {
-    const langMap: Record<string, string[]> = {
-      typescript: ['ts', 'tsx'],
-      javascript: ['js', 'jsx'],
-      python: ['py'],
-      go: ['go'],
-      java: ['java'],
-      rust: ['rs'],
-    };
-
-    return languages.some((lang) => {
-      const exts = langMap[lang.toLowerCase()] || [lang];
-      return exts.includes(ext);
-    });
-  }
-
-  private isTestFile(path: string): boolean {
-    const testPatterns = [
-      /\.test\.[tj]sx?$/,
-      /\.spec\.[tj]sx?$/,
-      /_test\.[tj]sx?$/,
-      /test_.*\.py$/,
-      /.*_test\.py$/,
-      /.*_test\.go$/,
-    ];
-
-    return testPatterns.some((pattern) => pattern.test(path));
-  }
-}
-
-/**
- * Extracted entity from source code
- */
-interface ExtractedEntity {
-  type: 'class' | 'function' | 'interface' | 'type' | 'variable' | 'module';
-  name: string;
-  line: number;
-  visibility: 'public' | 'private' | 'protected';
-  isAsync: boolean;
-}