kirograph 0.17.0 → 0.19.0

package/dist/security/integrator.js

@@ -0,0 +1,491 @@
+"use strict";
+var __create = Object.create;
+var __defProp = Object.defineProperty;
+var __getOwnPropDesc = Object.getOwnPropertyDescriptor;
+var __getOwnPropNames = Object.getOwnPropertyNames;
+var __getProtoOf = Object.getPrototypeOf;
+var __hasOwnProp = Object.prototype.hasOwnProperty;
+var __export = (target, all) => {
+  for (var name in all)
+    __defProp(target, name, { get: all[name], enumerable: true });
+};
+var __copyProps = (to, from, except, desc) => {
+  if (from && typeof from === "object" || typeof from === "function") {
+    for (let key of __getOwnPropNames(from))
+      if (!__hasOwnProp.call(to, key) && key !== except)
+        __defProp(to, key, { get: () => from[key], enumerable: !(desc = __getOwnPropDesc(from, key)) || desc.enumerable });
+  }
+  return to;
+};
+var __toESM = (mod, isNodeMode, target) => (target = mod != null ? __create(__getProtoOf(mod)) : {}, __copyProps(
+  // If the importer is in node compatibility mode or this is not an ESM
+  // file that has been converted to a CommonJS file using a Babel-
+  // compatible transform (i.e. "__esModule" has not been set), then set
+  // "default" to the CommonJS "module.exports" for node compatibility.
+  isNodeMode || !mod || !mod.__esModule ? __defProp(target, "default", { value: mod, enumerable: true }) : target,
+  mod
+));
+var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: true }), mod);
+var integrator_exports = {};
+__export(integrator_exports, {
+  DependencyGraphIntegrator: () => DependencyGraphIntegrator
+});
+module.exports = __toCommonJS(integrator_exports);
+var fs = __toESM(require("fs"));
+var path = __toESM(require("path"));
+var import_errors = require("../errors");
+function parseNpmLockTransitives(lockPath) {
+  const deps = [];
+  try {
+    const content = fs.readFileSync(lockPath, "utf8");
+    const lockData = JSON.parse(content);
+    if (typeof lockData !== "object" || lockData === null) return deps;
+    const packages = lockData.packages;
+    if (typeof packages !== "object" || packages === null) {
+      return parseNpmLockV1Transitives(lockData);
+    }
+    for (const [key, value] of Object.entries(packages)) {
+      if (key === "") continue;
+      if (typeof value !== "object" || value === null) continue;
+      const pkg = value;
+      const parentName = key.replace(/^.*node_modules\//, "");
+      if (!parentName) continue;
+      const allDeps = {};
+      for (const field of ["dependencies", "optionalDependencies", "peerDependencies"]) {
+        const fieldDeps = pkg[field];
+        if (typeof fieldDeps === "object" && fieldDeps !== null) {
+          Object.assign(allDeps, fieldDeps);
+        }
+      }
+      for (const childName of Object.keys(allDeps)) {
+        deps.push({ parent: parentName, child: childName });
+      }
+    }
+  } catch {
+  }
+  return deps;
+}
+function parseNpmLockV1Transitives(lockData) {
+  const deps = [];
+  const topDeps = lockData.dependencies;
+  if (typeof topDeps !== "object" || topDeps === null) return deps;
+  function recurse(parentDeps) {
+    for (const [name, value] of Object.entries(parentDeps)) {
+      if (typeof value !== "object" || value === null) continue;
+      const pkg = value;
+      const requires = pkg.requires;
+      if (typeof requires === "object" && requires !== null) {
+        for (const childName of Object.keys(requires)) {
+          deps.push({ parent: name, child: childName });
+        }
+      }
+      const nested = pkg.dependencies;
+      if (typeof nested === "object" && nested !== null) {
+        recurse(nested);
+      }
+    }
+  }
+  recurse(topDeps);
+  return deps;
+}
+function parseCargoLockTransitives(lockPath) {
+  const deps = [];
+  try {
+    const content = fs.readFileSync(lockPath, "utf8");
+    const lines = content.split("\n");
+    let currentName = null;
+    let inDeps = false;
+    for (const line of lines) {
+      const trimmed = line.trim();
+      if (trimmed === "[[package]]") {
+        currentName = null;
+        inDeps = false;
+        continue;
+      }
+      if (currentName === null) {
+        const nameMatch = trimmed.match(/^name\s*=\s*"([^"]+)"$/);
+        if (nameMatch) {
+          currentName = nameMatch[1];
+          continue;
+        }
+      }
+      if (currentName !== null && trimmed === "dependencies = [") {
+        inDeps = true;
+        continue;
+      }
+      if (inDeps) {
+        if (trimmed === "]") {
+          inDeps = false;
+          continue;
+        }
+        const depMatch = trimmed.match(/^\s*"([^"\s]+)/);
+        if (depMatch && currentName) {
+          deps.push({ parent: currentName, child: depMatch[1] });
+        }
+      }
+    }
+  } catch {
+  }
+  return deps;
+}
+function parseGoTransitives(_lockPath) {
+  return [];
+}
+function parsePipTransitives(_lockPath) {
+  return [];
+}
+function discoverLockFiles(projectRoot) {
+  const lockFiles = [];
+  const candidates = [
+    { ecosystem: "npm", filename: "package-lock.json", parser: parseNpmLockTransitives },
+    { ecosystem: "npm", filename: "yarn.lock", parser: parseNpmLockTransitives },
+    { ecosystem: "cargo", filename: "Cargo.lock", parser: parseCargoLockTransitives },
+    { ecosystem: "go", filename: "go.sum", parser: parseGoTransitives },
+    { ecosystem: "python", filename: "requirements.txt", parser: parsePipTransitives }
+  ];
+  for (const candidate of candidates) {
+    const lockPath = path.join(projectRoot, candidate.filename);
+    if (fs.existsSync(lockPath)) {
+      lockFiles.push({
+        ecosystem: candidate.ecosystem,
+        lockPath,
+        parser: candidate.parser
+      });
+    }
+  }
+  return lockFiles;
+}
+class DependencyGraphIntegrator {
+  constructor(db, projectRoot) {
+    this.db = db;
+    this.projectRoot = projectRoot;
+  }
+  /**
+   * Create import/reference edges between code symbols and Dependency_Nodes.
+   *
+   * Per Requirement 2.1: creates `imports` edges from file nodes that contain
+   * import statements resolving to a dependency → the Dependency_Node.
+   *
+   * Per Requirement 2.2: creates `references` edges from code symbols that
+   * reference classes/functions from a dependency → the Dependency_Node.
+   */
+  async integrate() {
+    let importsEdgesCreated = 0;
+    let referencesEdgesCreated = 0;
+    const rawDb = this.db.getRawDb();
+    const depRows = rawDb.all("SELECT node_id, package_name, ecosystem FROM sec_dependencies");
+    if (depRows.length === 0) {
+      return { importsEdgesCreated, referencesEdgesCreated };
+    }
+    const depByName = /* @__PURE__ */ new Map();
+    for (const row of depRows) {
+      depByName.set(row.package_name, row.node_id);
+    }
+    const importNodes = this.db.getNodesByKind("import");
+    const createdImportEdges = /* @__PURE__ */ new Set();
+    for (const importNode of importNodes) {
+      const specifier = importNode.name;
+      const matchedDepId = this.matchImportToDependency(specifier, depByName);
+      if (!matchedDepId) continue;
+      const fileNodeId = this.findFileNodeId(rawDb, importNode.filePath);
+      if (!fileNodeId) continue;
+      const edgeKey = `${fileNodeId}\u2192${matchedDepId}`;
+      if (createdImportEdges.has(edgeKey)) continue;
+      const edge = {
+        source: fileNodeId,
+        target: matchedDepId,
+        kind: "imports",
+        line: importNode.startLine,
+        confidence: "inferred",
+        confidenceScore: 0.9
+      };
+      this.db.insertEdge(edge);
+      createdImportEdges.add(edgeKey);
+      importsEdgesCreated++;
+    }
+    const codeKinds = /* @__PURE__ */ new Set(["function", "method", "class", "variable", "constant", "property"]);
+    const createdRefEdges = /* @__PURE__ */ new Set();
+    for (const importNode of importNodes) {
+      const specifier = importNode.name;
+      const matchedDepId = this.matchImportToDependency(specifier, depByName);
+      if (!matchedDepId) continue;
+      const fileNodes = this.db.getNodesByFile(importNode.filePath);
+      const codeSymbols = fileNodes.filter((n) => codeKinds.has(n.kind));
+      if (codeSymbols.length === 0) continue;
+      const symbolIds = codeSymbols.map((n) => n.id);
+      const edges = this.db.getEdgesForNodes(symbolIds);
+      for (const edge of edges) {
+        if ((edge.kind === "calls" || edge.kind === "references") && edge.target === importNode.id && symbolIds.includes(edge.source)) {
+          const refKey = `${edge.source}\u2192${matchedDepId}`;
+          if (createdRefEdges.has(refKey)) continue;
+          const refEdge = {
+            source: edge.source,
+            target: matchedDepId,
+            kind: "references",
+            confidence: "inferred",
+            confidenceScore: 0.8
+          };
+          this.db.insertEdge(refEdge);
+          createdRefEdges.add(refKey);
+          referencesEdgesCreated++;
+        }
+      }
+    }
+    return { importsEdgesCreated, referencesEdgesCreated };
+  }
+  /**
+   * Find the file node ID for a given file path.
+   * File nodes have kind='file' and their file_path matches.
+   */
+  findFileNodeId(rawDb, filePath) {
+    const row = rawDb.get(
+      "SELECT id FROM nodes WHERE kind = ? AND file_path = ? LIMIT 1",
+      ["file", filePath]
+    );
+    return row ? row.id : null;
+  }
+  /**
+   * Match an import specifier to a dependency node ID.
+   *
+   * Handles:
+   * - Exact match: `express` → dep:npm:express
+   * - Scoped packages: `@scope/pkg` → dep:npm:@scope/pkg
+   * - Subpath imports: `express/Router` → dep:npm:express
+   * - Scoped subpath: `@angular/core/testing` → dep:npm:@angular/core
+   * - Go modules: `github.com/gin-gonic/gin` → dep:go:github.com/gin-gonic/gin
+   * - Go subpath: `github.com/gin-gonic/gin/internal` → dep:go:github.com/gin-gonic/gin
+   */
+  matchImportToDependency(specifier, depByName) {
+    if (!specifier) return null;
+    if (specifier.startsWith(".") || specifier.startsWith("/")) return null;
+    if (depByName.has(specifier)) {
+      return depByName.get(specifier);
+    }
+    if (specifier.startsWith("@")) {
+      const parts = specifier.split("/");
+      if (parts.length >= 2) {
+        const scopedName = `${parts[0]}/${parts[1]}`;
+        if (depByName.has(scopedName)) {
+          return depByName.get(scopedName);
+        }
+      }
+    }
+    if (!specifier.startsWith("@")) {
+      const slashIdx = specifier.indexOf("/");
+      if (slashIdx > 0) {
+        const baseName = specifier.slice(0, slashIdx);
+        if (depByName.has(baseName)) {
+          return depByName.get(baseName);
+        }
+      }
+    }
+    if (specifier.includes(".") && specifier.includes("/")) {
+      const parts = specifier.split("/");
+      for (let i = parts.length - 1; i >= 2; i--) {
+        const prefix = parts.slice(0, i).join("/");
+        if (depByName.has(prefix)) {
+          return depByName.get(prefix);
+        }
+      }
+    }
+    return null;
+  }
+  /**
+   * Resolve transitive dependencies up to maxDepth levels.
+   *
+   * For each ecosystem with a lock file:
+   * 1. Parse the lock file to extract dependency relationships
+   * 2. Create `depends_on` edges between Dependency_Nodes
+   * 3. Traverse up to maxDepth levels of transitive depth
+   *
+   * If a lock file is missing for an ecosystem, mark all dependencies of that
+   * ecosystem with `transitive_status: 'incomplete'` and log a warning.
+   *
+   * @param maxDepth - Maximum levels of transitive depth to resolve (default: 10)
+   */
+  async resolveTransitives(maxDepth = 10) {
+    let dependsOnEdgesCreated = 0;
+    const incompleteNodes = [];
+    const rawDb = this.db.getRawDb();
+    const depRows = rawDb.all("SELECT node_id, package_name, ecosystem FROM sec_dependencies");
+    if (depRows.length === 0) {
+      return { dependsOnEdgesCreated, incompleteNodes };
+    }
+    const depsByEcosystem = /* @__PURE__ */ new Map();
+    for (const row of depRows) {
+      if (!depsByEcosystem.has(row.ecosystem)) {
+        depsByEcosystem.set(row.ecosystem, /* @__PURE__ */ new Map());
+      }
+      depsByEcosystem.get(row.ecosystem).set(row.package_name, row.node_id);
+    }
+    const lockFiles = discoverLockFiles(this.projectRoot);
+    const ecosystemsWithLockFile = new Set(lockFiles.map((lf) => lf.ecosystem));
+    for (const [ecosystem, depsMap] of depsByEcosystem) {
+      if (!ecosystemsWithLockFile.has(ecosystem)) {
+        for (const [pkgName, nodeId] of depsMap) {
+          rawDb.run(
+            `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,
+            [nodeId]
+          );
+          incompleteNodes.push(nodeId);
+          (0, import_errors.logWarn)(
+            `[sec:integrator] Transitive resolution incomplete for "${pkgName}" (${ecosystem}): no lock file found`
+          );
+        }
+      }
+    }
+    for (const lockFile of lockFiles) {
+      const transitives = lockFile.parser(lockFile.lockPath);
+      const ecosystemDeps = depsByEcosystem.get(lockFile.ecosystem);
+      if (!ecosystemDeps) continue;
+      if (transitives.length === 0 && ecosystemDeps.size > 0) {
+        if (lockFile.ecosystem === "go" || lockFile.ecosystem === "python") {
+          for (const [pkgName, nodeId] of ecosystemDeps) {
+            rawDb.run(
+              `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,
+              [nodeId]
+            );
+            incompleteNodes.push(nodeId);
+            (0, import_errors.logWarn)(
+              `[sec:integrator] Transitive resolution incomplete for "${pkgName}" (${lockFile.ecosystem}): dependency tree not resolvable from lock file`
+            );
+          }
+        }
+        continue;
+      }
+      const adjacency = /* @__PURE__ */ new Map();
+      for (const { parent, child } of transitives) {
+        if (!adjacency.has(parent)) {
+          adjacency.set(parent, /* @__PURE__ */ new Set());
+        }
+        adjacency.get(parent).add(child);
+      }
+      const createdEdges = /* @__PURE__ */ new Set();
+      for (const [pkgName, nodeId] of ecosystemDeps) {
+        const visited = /* @__PURE__ */ new Set([pkgName]);
+        let frontier = [pkgName];
+        let depth = 0;
+        while (frontier.length > 0 && depth < maxDepth) {
+          const nextFrontier = [];
+          depth++;
+          for (const current of frontier) {
+            const children = adjacency.get(current);
+            if (!children) continue;
+            for (const child of children) {
+              if (visited.has(child)) continue;
+              visited.add(child);
+              const childNodeId = ecosystemDeps.get(child);
+              const parentNodeId = current === pkgName ? nodeId : ecosystemDeps.get(current);
+              if (parentNodeId && childNodeId) {
+                const edgeKey = `${parentNodeId}->${childNodeId}`;
+                if (!createdEdges.has(edgeKey)) {
+                  const edge = {
+                    source: parentNodeId,
+                    target: childNodeId,
+                    kind: "depends_on",
+                    confidence: "inferred",
+                    confidenceScore: 1
+                  };
+                  this.db.insertEdge(edge);
+                  createdEdges.add(edgeKey);
+                  dependsOnEdgesCreated++;
+                }
+              }
+              nextFrontier.push(child);
+            }
+          }
+          frontier = nextFrontier;
+        }
+      }
+    }
+    return { dependsOnEdgesCreated, incompleteNodes };
+  }
+  /**
+   * Remove orphaned Dependency_Nodes and their edges.
+   *
+   * A Dependency_Node is orphaned if:
+   * 1. It has no `declared_in` edges (manifest no longer declares it), OR
+   * 2. None of its source manifests still exist on disk
+   *
+   * Also removes transitive Dependency_Nodes that are no longer reachable from
+   * any remaining direct dependency via `depends_on` edges.
+   *
+   * @param manifestExists - Optional function to check if a manifest path exists.
+   *   Defaults to fs.existsSync. Useful for testing.
+   */
+  async cleanup(manifestExists) {
+    let nodesRemoved = 0;
+    let edgesRemoved = 0;
+    const rawDb = this.db.getRawDb();
+    const checkExists = manifestExists ?? ((p) => fs.existsSync(p));
+    const orphanedByEdge = rawDb.all(
+      `SELECT sd.node_id FROM sec_dependencies sd
+       WHERE NOT EXISTS (
+         SELECT 1 FROM edges e
+         WHERE e.source = sd.node_id AND e.kind = 'declared_in'
+       )`
+    );
+    const orphanedNodeIds = new Set(orphanedByEdge.map((r) => r.node_id));
+    const allDeps = rawDb.all(
+      `SELECT node_id, source_manifests FROM sec_dependencies`
+    );
+    for (const dep of allDeps) {
+      if (orphanedNodeIds.has(dep.node_id)) continue;
+      const sourceManifests = JSON.parse(dep.source_manifests);
+      const hasValidManifest = sourceManifests.some((manifest) => {
+        const absolutePath = path.isAbsolute(manifest) ? manifest : path.join(this.projectRoot, manifest);
+        return checkExists(absolutePath);
+      });
+      if (!hasValidManifest) {
+        orphanedNodeIds.add(dep.node_id);
+      }
+    }
+    const remainingNodeIds = new Set(
+      allDeps.filter((d) => !orphanedNodeIds.has(d.node_id)).map((d) => d.node_id)
+    );
+    const reachableFromDirect = new Set(remainingNodeIds);
+    let frontier = [...remainingNodeIds];
+    while (frontier.length > 0) {
+      const placeholders = frontier.map(() => "?").join(",");
+      const nextRows = rawDb.all(
+        `SELECT DISTINCT target FROM edges WHERE source IN (${placeholders}) AND kind = 'depends_on'`,
+        frontier
+      );
+      frontier = [];
+      for (const row of nextRows) {
+        if (!reachableFromDirect.has(row.target)) {
+          reachableFromDirect.add(row.target);
+          frontier.push(row.target);
+        }
+      }
+    }
+    for (const dep of allDeps) {
+      if (!orphanedNodeIds.has(dep.node_id) && !reachableFromDirect.has(dep.node_id)) {
+        orphanedNodeIds.add(dep.node_id);
+      }
+    }
+    if (orphanedNodeIds.size === 0) {
+      return { nodesRemoved: 0, edgesRemoved: 0 };
+    }
+    const orphanedIds = [...orphanedNodeIds];
+    for (const nodeId of orphanedIds) {
+      const edgeCount = rawDb.get(
+        `SELECT COUNT(*) as c FROM edges
+         WHERE source = ? OR target = ?`,
+        [nodeId, nodeId]
+      );
+      edgesRemoved += edgeCount?.c ?? 0;
+      rawDb.run("DELETE FROM edges WHERE source = ? OR target = ?", [nodeId, nodeId]);
+      rawDb.run("DELETE FROM sec_dependencies WHERE node_id = ?", [nodeId]);
+      rawDb.run("DELETE FROM nodes WHERE id = ?", [nodeId]);
+      rawDb.run("DELETE FROM nodes_fts WHERE id = ?", [nodeId]);
+      nodesRemoved++;
+    }
+    return { nodesRemoved, edgesRemoved };
+  }
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  DependencyGraphIntegrator
+});
+//# sourceMappingURL=integrator.js.map

package/dist/security/integrator.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/security/integrator.ts"],
+  "sourcesContent": ["/**\n * DependencyGraphIntegrator\n *\n * Links dependency nodes to code symbols via import and reference edges,\n * resolves transitive dependencies from lock files, and cleans up orphaned nodes.\n *\n * Integration flow:\n * 1. integrate() \u2014 Scan file nodes for import statements resolving to dependencies,\n *    create `imports` and `references` edges.\n * 2. resolveTransitives(maxDepth) \u2014 Parse lock files to discover transitive dependency\n *    relationships, create `depends_on` edges between Dependency_Nodes.\n * 3. cleanup() \u2014 Remove orphaned Dependency_Nodes no longer declared in any manifest.\n */\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport type { GraphDatabase } from '../db/database';\nimport type { Edge } from '../types';\nimport type { IntegrationResult, TransitiveResult, CleanupResult } from './types';\nimport { logWarn } from '../errors';\n\n// \u2500\u2500 Lock File Parsers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Transitive dependency relationship: parent depends on child.\n */\ninterface TransitiveDep {\n  parent: string;\n  child: string;\n}\n\n/**\n * Parse package-lock.json (v2/v3) to extract transitive dependency relationships.\n * Returns pairs of (parent, child) where parent depends on child.\n */\nfunction parseNpmLockTransitives(lockPath: string): TransitiveDep[] {\n  const deps: TransitiveDep[] = [];\n  try {\n    const content = fs.readFileSync(lockPath, 'utf8');\n    const lockData = JSON.parse(content);\n\n    if (typeof lockData !== 'object' || lockData === null) return deps;\n\n    const packages = lockData.packages;\n    if (typeof packages !== 'object' || packages === null) {\n      // Try lockfileVersion 1 format\n      return parseNpmLockV1Transitives(lockData);\n    }\n\n    // lockfileVersion 2/3: packages field with nested node_modules paths\n    for (const [key, value] of Object.entries(packages as Record<string, unknown>)) {\n      if (key === '') continue; // skip root\n      if (typeof value !== 'object' || value === null) continue;\n      const pkg = value as Record<string, unknown>;\n\n      // Extract the package name from the key\n      const parentName = key.replace(/^.*node_modules\\//, '');\n      if (!parentName) continue;\n\n      // Extract this package's dependencies\n      const allDeps: Record<string, unknown> = {};\n      for (const field of ['dependencies', 'optionalDependencies', 'peerDependencies']) {\n        const fieldDeps = pkg[field];\n        if (typeof fieldDeps === 'object' && fieldDeps !== null) {\n          Object.assign(allDeps, fieldDeps);\n        }\n      }\n\n      for (const childName of Object.keys(allDeps)) {\n        deps.push({ parent: parentName, child: childName });\n      }\n    }\n  } catch {\n    // Lock file parse failure \u2014 return empty\n  }\n  return deps;\n}\n\n/**\n * Parse lockfileVersion 1 format (nested dependencies object).\n */\nfunction parseNpmLockV1Transitives(lockData: Record<string, unknown>): TransitiveDep[] {\n  const deps: TransitiveDep[] = [];\n  const topDeps = lockData.dependencies;\n  if (typeof topDeps !== 'object' || topDeps === null) return deps;\n\n  function recurse(parentDeps: Record<string, unknown>): void {\n    for (const [name, value] of Object.entries(parentDeps)) {\n      if (typeof value !== 'object' || value === null) continue;\n      const pkg = value as Record<string, unknown>;\n\n      // Check for requires (direct dependencies of this package)\n      const requires = pkg.requires;\n      if (typeof requires === 'object' && requires !== null) {\n        for (const childName of Object.keys(requires as Record<string, unknown>)) {\n          deps.push({ parent: name, child: childName });\n        }\n      }\n\n      // Recurse into nested dependencies\n      const nested = pkg.dependencies;\n      if (typeof nested === 'object' && nested !== null) {\n        recurse(nested as Record<string, unknown>);\n      }\n    }\n  }\n\n  recurse(topDeps as Record<string, unknown>);\n  return deps;\n}\n\n/**\n * Parse Cargo.lock to extract transitive dependency relationships.\n * Cargo.lock [[package]] blocks have a `dependencies` field listing direct deps.\n */\nfunction parseCargoLockTransitives(lockPath: string): TransitiveDep[] {\n  const deps: TransitiveDep[] = [];\n  try {\n    const content = fs.readFileSync(lockPath, 'utf8');\n    const lines = content.split('\\n');\n\n    let currentName: string | null = null;\n    let inDeps = false;\n\n    for (const line of lines) {\n      const trimmed = line.trim();\n\n      if (trimmed === '[[package]]') {\n        currentName = null;\n        inDeps = false;\n        continue;\n      }\n\n      if (currentName === null) {\n        const nameMatch = trimmed.match(/^name\\s*=\\s*\"([^\"]+)\"$/);\n        if (nameMatch) {\n          currentName = nameMatch[1];\n          continue;\n        }\n      }\n\n      if (currentName !== null && trimmed === 'dependencies = [') {\n        inDeps = true;\n        continue;\n      }\n\n      if (inDeps) {\n        if (trimmed === ']') {\n          inDeps = false;\n          continue;\n        }\n        // Lines like: \"serde_derive 1.0.193 (registry+...)\",\n        // or simply: \"serde_derive\",\n        const depMatch = trimmed.match(/^\\s*\"([^\"\\s]+)/);\n        if (depMatch && currentName) {\n          deps.push({ parent: currentName, child: depMatch[1] });\n        }\n      }\n    }\n  } catch {\n    // Lock file parse failure \u2014 return empty\n  }\n  return deps;\n}\n\n/**\n * Parse go.sum to extract module dependency relationships.\n * go.sum doesn't directly encode dependency trees, so we parse go.mod\n * for the require directives. For transitive resolution, we'd need\n * `go mod graph` output, but for the MVP we mark Go deps as incomplete\n * if no explicit dependency tree is available.\n *\n * Returns empty \u2014 Go transitive resolution requires `go mod graph` which\n * is not available at index time. Nodes will be marked incomplete.\n */\nfunction parseGoTransitives(_lockPath: string): TransitiveDep[] {\n  // Go modules don't have a lock file that encodes the dependency tree.\n  // go.sum only provides checksums. Full transitive resolution requires\n  // running `go mod graph` which is out of scope for static analysis.\n  return [];\n}\n\n/**\n * Parse pip's requirements files for transitive dependencies.\n * pip doesn't have a standard lock file with dependency trees.\n * Returns empty \u2014 nodes will be marked incomplete.\n */\nfunction parsePipTransitives(_lockPath: string): TransitiveDep[] {\n  return [];\n}\n\n// \u2500\u2500 Lock File Discovery \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\ninterface LockFileInfo {\n  ecosystem: string;\n  lockPath: string;\n  parser: (lockPath: string) => TransitiveDep[];\n}\n\n/**\n * Discover lock files in the project root for each ecosystem.\n */\nfunction discoverLockFiles(projectRoot: string): LockFileInfo[] {\n  const lockFiles: LockFileInfo[] = [];\n\n  const candidates: Array<{ ecosystem: string; filename: string; parser: (p: string) => TransitiveDep[] }> = [\n    { ecosystem: 'npm', filename: 'package-lock.json', parser: parseNpmLockTransitives },\n    { ecosystem: 'npm', filename: 'yarn.lock', parser: parseNpmLockTransitives },\n    { ecosystem: 'cargo', filename: 'Cargo.lock', parser: parseCargoLockTransitives },\n    { ecosystem: 'go', filename: 'go.sum', parser: parseGoTransitives },\n    { ecosystem: 'python', filename: 'requirements.txt', parser: parsePipTransitives },\n  ];\n\n  for (const candidate of candidates) {\n    const lockPath = path.join(projectRoot, candidate.filename);\n    if (fs.existsSync(lockPath)) {\n      lockFiles.push({\n        ecosystem: candidate.ecosystem,\n        lockPath,\n        parser: candidate.parser,\n      });\n    }\n  }\n\n  return lockFiles;\n}\n\n// \u2500\u2500 DependencyGraphIntegrator Class \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport class DependencyGraphIntegrator {\n  private readonly db: GraphDatabase;\n  private readonly projectRoot: string;\n\n  constructor(db: GraphDatabase, projectRoot: string) {\n    this.db = db;\n    this.projectRoot = projectRoot;\n  }\n\n  /**\n   * Create import/reference edges between code symbols and Dependency_Nodes.\n   *\n   * Per Requirement 2.1: creates `imports` edges from file nodes that contain\n   * import statements resolving to a dependency \u2192 the Dependency_Node.\n   *\n   * Per Requirement 2.2: creates `references` edges from code symbols that\n   * reference classes/functions from a dependency \u2192 the Dependency_Node.\n   */\n  async integrate(): Promise<IntegrationResult> {\n    let importsEdgesCreated = 0;\n    let referencesEdgesCreated = 0;\n\n    const rawDb = this.db.getRawDb();\n\n    // Get all dependency nodes with their package names and ecosystems\n    const depRows: Array<{ node_id: string; package_name: string; ecosystem: string }> =\n      rawDb.all('SELECT node_id, package_name, ecosystem FROM sec_dependencies');\n\n    if (depRows.length === 0) {\n      return { importsEdgesCreated, referencesEdgesCreated };\n    }\n\n    // Build a lookup map: package name \u2192 dependency node ID\n    const depByName = new Map<string, string>();\n    for (const row of depRows) {\n      depByName.set(row.package_name, row.node_id);\n    }\n\n    // \u2500\u2500 Step 1: Create `imports` edges (file \u2192 dependency) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    // Scan import nodes. The import node's `name` field contains the module\n    // specifier (e.g., 'express', '@nestjs/core', 'github.com/gin-gonic/gin').\n    // For each match, create an edge from the FILE node to the Dependency_Node.\n    const importNodes = this.db.getNodesByKind('import');\n\n    // Track (file, dep) pairs to avoid duplicate edges\n    const createdImportEdges = new Set<string>();\n\n    for (const importNode of importNodes) {\n      // Use the import node's `name` field which is the raw module specifier\n      const specifier = importNode.name;\n\n      const matchedDepId = this.matchImportToDependency(specifier, depByName);\n      if (!matchedDepId) continue;\n\n      // Find the file node for this import's file path\n      const fileNodeId = this.findFileNodeId(rawDb, importNode.filePath);\n      if (!fileNodeId) continue;\n\n      const edgeKey = `${fileNodeId}\u2192${matchedDepId}`;\n      if (createdImportEdges.has(edgeKey)) continue;\n\n      const edge: Edge = {\n        source: fileNodeId,\n        target: matchedDepId,\n        kind: 'imports',\n        line: importNode.startLine,\n        confidence: 'inferred',\n        confidenceScore: 0.9,\n      };\n      this.db.insertEdge(edge);\n      createdImportEdges.add(edgeKey);\n      importsEdgesCreated++;\n    }\n\n    // \u2500\u2500 Step 2: Create `references` edges (code symbol \u2192 dependency) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    // For each import node that matched a dependency, find code symbols in the\n    // same file that call or reference that import node. Those symbols effectively\n    // reference the dependency.\n    const codeKinds = new Set(['function', 'method', 'class', 'variable', 'constant', 'property']);\n    const createdRefEdges = new Set<string>();\n\n    for (const importNode of importNodes) {\n      const specifier = importNode.name;\n      const matchedDepId = this.matchImportToDependency(specifier, depByName);\n      if (!matchedDepId) continue;\n\n      // Get all nodes in the same file\n      const fileNodes = this.db.getNodesByFile(importNode.filePath);\n      const codeSymbols = fileNodes.filter(n => codeKinds.has(n.kind));\n      if (codeSymbols.length === 0) continue;\n\n      // Check edges from code symbols to this import node\n      const symbolIds = codeSymbols.map(n => n.id);\n      const edges = this.db.getEdgesForNodes(symbolIds);\n\n      for (const edge of edges) {\n        // A code symbol calls or references the import node \u2192 it references the dependency\n        if (\n          (edge.kind === 'calls' || edge.kind === 'references') &&\n          edge.target === importNode.id &&\n          symbolIds.includes(edge.source)\n        ) {\n          const refKey = `${edge.source}\u2192${matchedDepId}`;\n          if (createdRefEdges.has(refKey)) continue;\n\n          const refEdge: Edge = {\n            source: edge.source,\n            target: matchedDepId,\n            kind: 'references',\n            confidence: 'inferred',\n            confidenceScore: 0.8,\n          };\n          this.db.insertEdge(refEdge);\n          createdRefEdges.add(refKey);\n          referencesEdgesCreated++;\n        }\n      }\n    }\n\n    return { importsEdgesCreated, referencesEdgesCreated };\n  }\n\n  /**\n   * Find the file node ID for a given file path.\n   * File nodes have kind='file' and their file_path matches.\n   */\n  private findFileNodeId(rawDb: any, filePath: string): string | null {\n    const row = rawDb.get(\n      'SELECT id FROM nodes WHERE kind = ? AND file_path = ? LIMIT 1',\n      ['file', filePath],\n    );\n    return row ? row.id : null;\n  }\n\n  /**\n   * Match an import specifier to a dependency node ID.\n   *\n   * Handles:\n   * - Exact match: `express` \u2192 dep:npm:express\n   * - Scoped packages: `@scope/pkg` \u2192 dep:npm:@scope/pkg\n   * - Subpath imports: `express/Router` \u2192 dep:npm:express\n   * - Scoped subpath: `@angular/core/testing` \u2192 dep:npm:@angular/core\n   * - Go modules: `github.com/gin-gonic/gin` \u2192 dep:go:github.com/gin-gonic/gin\n   * - Go subpath: `github.com/gin-gonic/gin/internal` \u2192 dep:go:github.com/gin-gonic/gin\n   */\n  private matchImportToDependency(\n    specifier: string,\n    depByName: Map<string, string>,\n  ): string | null {\n    if (!specifier) return null;\n\n    // Skip relative imports\n    if (specifier.startsWith('.') || specifier.startsWith('/')) return null;\n\n    // Direct match\n    if (depByName.has(specifier)) {\n      return depByName.get(specifier)!;\n    }\n\n    // For scoped packages: @scope/name/subpath \u2192 @scope/name\n    if (specifier.startsWith('@')) {\n      const parts = specifier.split('/');\n      if (parts.length >= 2) {\n        const scopedName = `${parts[0]}/${parts[1]}`;\n        if (depByName.has(scopedName)) {\n          return depByName.get(scopedName)!;\n        }\n      }\n    }\n\n    // For unscoped packages: name/subpath \u2192 name\n    if (!specifier.startsWith('@')) {\n      const slashIdx = specifier.indexOf('/');\n      if (slashIdx > 0) {\n        const baseName = specifier.slice(0, slashIdx);\n        if (depByName.has(baseName)) {\n          return depByName.get(baseName)!;\n        }\n      }\n    }\n\n    // Go module path matching: try progressively shorter prefixes\n    // e.g. github.com/gin-gonic/gin/internal \u2192 github.com/gin-gonic/gin\n    if (specifier.includes('.') && specifier.includes('/')) {\n      const parts = specifier.split('/');\n      for (let i = parts.length - 1; i >= 2; i--) {\n        const prefix = parts.slice(0, i).join('/');\n        if (depByName.has(prefix)) {\n          return depByName.get(prefix)!;\n        }\n      }\n    }\n\n    return null;\n  }\n\n  /**\n   * Resolve transitive dependencies up to maxDepth levels.\n   *\n   * For each ecosystem with a lock file:\n   * 1. Parse the lock file to extract dependency relationships\n   * 2. Create `depends_on` edges between Dependency_Nodes\n   * 3. Traverse up to maxDepth levels of transitive depth\n   *\n   * If a lock file is missing for an ecosystem, mark all dependencies of that\n   * ecosystem with `transitive_status: 'incomplete'` and log a warning.\n   *\n   * @param maxDepth - Maximum levels of transitive depth to resolve (default: 10)\n   */\n  async resolveTransitives(maxDepth: number = 10): Promise<TransitiveResult> {\n    let dependsOnEdgesCreated = 0;\n    const incompleteNodes: string[] = [];\n    const rawDb = this.db.getRawDb();\n\n    // Get all dependency nodes grouped by ecosystem\n    const depRows: Array<{ node_id: string; package_name: string; ecosystem: string }> =\n      rawDb.all('SELECT node_id, package_name, ecosystem FROM sec_dependencies');\n\n    if (depRows.length === 0) {\n      return { dependsOnEdgesCreated, incompleteNodes };\n    }\n\n    // Group dependencies by ecosystem\n    const depsByEcosystem = new Map<string, Map<string, string>>();\n    for (const row of depRows) {\n      if (!depsByEcosystem.has(row.ecosystem)) {\n        depsByEcosystem.set(row.ecosystem, new Map());\n      }\n      depsByEcosystem.get(row.ecosystem)!.set(row.package_name, row.node_id);\n    }\n\n    // Discover available lock files\n    const lockFiles = discoverLockFiles(this.projectRoot);\n    const ecosystemsWithLockFile = new Set(lockFiles.map(lf => lf.ecosystem));\n\n    // Mark ecosystems without lock files as incomplete\n    for (const [ecosystem, depsMap] of depsByEcosystem) {\n      if (!ecosystemsWithLockFile.has(ecosystem)) {\n        // No lock file for this ecosystem \u2014 mark all deps as incomplete\n        for (const [pkgName, nodeId] of depsMap) {\n          rawDb.run(\n            `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,\n            [nodeId],\n          );\n          incompleteNodes.push(nodeId);\n          logWarn(\n            `[sec:integrator] Transitive resolution incomplete for \"${pkgName}\" (${ecosystem}): ` +\n            `no lock file found`,\n          );\n        }\n      }\n    }\n\n    // Parse each lock file and create depends_on edges\n    for (const lockFile of lockFiles) {\n      const transitives = lockFile.parser(lockFile.lockPath);\n      const ecosystemDeps = depsByEcosystem.get(lockFile.ecosystem);\n      if (!ecosystemDeps) continue;\n\n      if (transitives.length === 0 && ecosystemDeps.size > 0) {\n        // Lock file exists but yielded no transitive info (e.g., go.sum)\n        // Mark deps as incomplete if the parser couldn't extract tree info\n        if (lockFile.ecosystem === 'go' || lockFile.ecosystem === 'python') {\n          for (const [pkgName, nodeId] of ecosystemDeps) {\n            rawDb.run(\n              `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,\n              [nodeId],\n            );\n            incompleteNodes.push(nodeId);\n            logWarn(\n              `[sec:integrator] Transitive resolution incomplete for \"${pkgName}\" (${lockFile.ecosystem}): ` +\n              `dependency tree not resolvable from lock file`,\n            );\n          }\n        }\n        continue;\n      }\n\n      // Build adjacency list from transitive relationships\n      const adjacency = new Map<string, Set<string>>();\n      for (const { parent, child } of transitives) {\n        if (!adjacency.has(parent)) {\n          adjacency.set(parent, new Set());\n        }\n        adjacency.get(parent)!.add(child);\n      }\n\n      // BFS from each direct dependency up to maxDepth levels\n      // Create depends_on edges only between nodes that exist in our dep graph\n      const createdEdges = new Set<string>();\n\n      for (const [pkgName, nodeId] of ecosystemDeps) {\n        const visited = new Set<string>([pkgName]);\n        let frontier = [pkgName];\n        let depth = 0;\n\n        while (frontier.length > 0 && depth < maxDepth) {\n          const nextFrontier: string[] = [];\n          depth++;\n\n          for (const current of frontier) {\n            const children = adjacency.get(current);\n            if (!children) continue;\n\n            for (const child of children) {\n              if (visited.has(child)) continue;\n              visited.add(child);\n\n              // Create depends_on edge if the child is a known dependency node\n              const childNodeId = ecosystemDeps.get(child);\n              const parentNodeId = current === pkgName ? nodeId : ecosystemDeps.get(current);\n\n              if (parentNodeId && childNodeId) {\n                const edgeKey = `${parentNodeId}->${childNodeId}`;\n                if (!createdEdges.has(edgeKey)) {\n                  const edge: Edge = {\n                    source: parentNodeId,\n                    target: childNodeId,\n                    kind: 'depends_on',\n                    confidence: 'inferred',\n                    confidenceScore: 1.0,\n                  };\n                  this.db.insertEdge(edge);\n                  createdEdges.add(edgeKey);\n                  dependsOnEdgesCreated++;\n                }\n              }\n\n              nextFrontier.push(child);\n            }\n          }\n\n          frontier = nextFrontier;\n        }\n      }\n    }\n\n    return { dependsOnEdgesCreated, incompleteNodes };\n  }\n\n  /**\n   * Remove orphaned Dependency_Nodes and their edges.\n   *\n   * A Dependency_Node is orphaned if:\n   * 1. It has no `declared_in` edges (manifest no longer declares it), OR\n   * 2. None of its source manifests still exist on disk\n   *\n   * Also removes transitive Dependency_Nodes that are no longer reachable from\n   * any remaining direct dependency via `depends_on` edges.\n   *\n   * @param manifestExists - Optional function to check if a manifest path exists.\n   *   Defaults to fs.existsSync. Useful for testing.\n   */\n  async cleanup(manifestExists?: (absolutePath: string) => boolean): Promise<CleanupResult> {\n    let nodesRemoved = 0;\n    let edgesRemoved = 0;\n    const rawDb = this.db.getRawDb();\n    const checkExists = manifestExists ?? ((p: string) => fs.existsSync(p));\n\n    // Step 1: Find dependency nodes that are orphaned because they have no\n    // declared_in edges (manifest no longer declares them)\n    const orphanedByEdge: Array<{ node_id: string }> = rawDb.all(\n      `SELECT sd.node_id FROM sec_dependencies sd\n       WHERE NOT EXISTS (\n         SELECT 1 FROM edges e\n         WHERE e.source = sd.node_id AND e.kind = 'declared_in'\n       )`,\n    );\n\n    const orphanedNodeIds = new Set<string>(orphanedByEdge.map(r => r.node_id));\n\n    // Step 2: Also check if source manifests still exist on disk\n    const allDeps: Array<{ node_id: string; source_manifests: string }> = rawDb.all(\n      `SELECT node_id, source_manifests FROM sec_dependencies`,\n    );\n\n    for (const dep of allDeps) {\n      if (orphanedNodeIds.has(dep.node_id)) continue; // already marked\n\n      const sourceManifests: string[] = JSON.parse(dep.source_manifests);\n      const hasValidManifest = sourceManifests.some(manifest => {\n        const absolutePath = path.isAbsolute(manifest)\n          ? manifest\n          : path.join(this.projectRoot, manifest);\n        return checkExists(absolutePath);\n      });\n\n      if (!hasValidManifest) {\n        orphanedNodeIds.add(dep.node_id);\n      }\n    }\n\n    // Step 3: Find transitive Dependency_Nodes no longer reachable from any\n    // remaining direct dependency via `depends_on` edges\n    const remainingNodeIds = new Set<string>(\n      allDeps\n        .filter(d => !orphanedNodeIds.has(d.node_id))\n        .map(d => d.node_id),\n    );\n\n    // BFS from remaining nodes following `depends_on` edges to find all reachable transitives\n    const reachableFromDirect = new Set<string>(remainingNodeIds);\n    let frontier = [...remainingNodeIds];\n\n    while (frontier.length > 0) {\n      const placeholders = frontier.map(() => '?').join(',');\n      const nextRows: Array<{ target: string }> = rawDb.all(\n        `SELECT DISTINCT target FROM edges WHERE source IN (${placeholders}) AND kind = 'depends_on'`,\n        frontier,\n      );\n\n      frontier = [];\n      for (const row of nextRows) {\n        if (!reachableFromDirect.has(row.target)) {\n          reachableFromDirect.add(row.target);\n          frontier.push(row.target);\n        }\n      }\n    }\n\n    // Any dependency node that is NOT reachable from a remaining direct dependency is also orphaned\n    for (const dep of allDeps) {\n      if (!orphanedNodeIds.has(dep.node_id) && !reachableFromDirect.has(dep.node_id)) {\n        orphanedNodeIds.add(dep.node_id);\n      }\n    }\n\n    if (orphanedNodeIds.size === 0) {\n      return { nodesRemoved: 0, edgesRemoved: 0 };\n    }\n\n    // Step 4: Remove orphaned nodes and their edges\n    const orphanedIds = [...orphanedNodeIds];\n\n    for (const nodeId of orphanedIds) {\n      // Count edges being removed\n      const edgeCount = rawDb.get(\n        `SELECT COUNT(*) as c FROM edges\n         WHERE source = ? OR target = ?`,\n        [nodeId, nodeId],\n      );\n      edgesRemoved += edgeCount?.c ?? 0;\n\n      // Delete edges connected to this node\n      rawDb.run('DELETE FROM edges WHERE source = ? OR target = ?', [nodeId, nodeId]);\n\n      // Remove from sec_dependencies (explicit delete before nodes for clarity)\n      rawDb.run('DELETE FROM sec_dependencies WHERE node_id = ?', [nodeId]);\n\n      // Remove from nodes table\n      rawDb.run('DELETE FROM nodes WHERE id = ?', [nodeId]);\n\n      // Clean up FTS entries\n      rawDb.run('DELETE FROM nodes_fts WHERE id = ?', [nodeId]);\n\n      nodesRemoved++;\n    }\n\n    return { nodesRemoved, edgesRemoved };\n  }\n}\n"],
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