agentic-qe 3.6.11 → 3.6.13

package/v3/dist/cli/bundle.js

@@ -149,7 +149,7 @@ var init_constants = __esm({
       /**
        * Vector dimension for coverage analysis embeddings.
        */
-      COVERAGE_VECTOR_DIMENSION: 128
+      COVERAGE_VECTOR_DIMENSION: 768
     };
     AGENT_CONSTANTS = {
       /**
@@ -1595,7 +1595,10 @@ var init_unified_memory_hnsw = __esm({
       search(query, k68) {
         if (this.ids.length === 0) return [];
         const actualK = Math.min(k68, this.ids.length);
-        if (ruvectorDifferentiableSearch && this.vectors.length > 0) {
+        const storedDim = this.vectors.length > 0 ? this.vectors[0].length : 0;
+        const queryDim = query.length;
+        const dimensionsMatch = storedDim === queryDim;
+        if (ruvectorDifferentiableSearch && this.vectors.length > 0 && dimensionsMatch) {
           const queryF322 = new Float32Array(query);
           const queryNorm2 = computeNorm(queryF322);
           const result = ruvectorDifferentiableSearch(
@@ -1613,10 +1616,20 @@ var init_unified_memory_hnsw = __esm({
         const queryNorm = computeNorm(queryF32);
         const scored = [];
         for (let i58 = 0; i58 < this.ids.length; i58++) {
-          scored.push({
-            id: this.ids[i58],
-            score: fastCosine(queryF32, this.vectors[i58], queryNorm, this.norms[i58])
-          });
+          const vec = this.vectors[i58];
+          if (vec.length !== queryF32.length) {
+            if (i58 === 0) {
+              console.warn(
+                `[RuvectorFlatIndex] Dimension mismatch: query=${queryF32.length}, stored=${vec.length}. Skipping ${this.ids.length} mismatched vectors. Re-index with correct dimensions.`
+              );
+            }
+            continue;
+          } else {
+            scored.push({
+              id: this.ids[i58],
+              score: fastCosine(queryF32, vec, queryNorm, this.norms[i58])
+            });
+          }
         }
         scored.sort((a37, b68) => b68.score - a37.score);
         return scored.slice(0, actualK);
@@ -8717,7 +8730,7 @@ function createHNSWIndex(memory, config) {
   return new HNSWIndex(memory, config);
 }
 async function benchmarkHNSW(index, vectorCount = 1e4, searchCount = 1e3) {
-  const dimensions = 128;
+  const dimensions = 768;
   const startInsert = performance.now();
   for (let i58 = 0; i58 < vectorCount; i58++) {
     const vector = Array.from({ length: dimensions }, () => Math.random());
@@ -8746,7 +8759,7 @@ var init_hnsw_index = __esm({
     QEGNNEmbeddingIndexClass = null;
     ruvectorLoaded = false;
     DEFAULT_HNSW_CONFIG = {
-      dimensions: 128,
+      dimensions: 768,
       M: 16,
       efConstruction: 200,
       efSearch: 100,
@@ -8998,7 +9011,7 @@ var init_hnsw_index = __esm({
       /**
        * Validate and auto-resize vectors to match HNSW configured dimensions.
        * Fix #279: Prevents Rust WASM panic when RealEmbeddings (768-dim) are
-       * passed to a 128-dim HNSW index.
+       * passed to a mismatched-dim HNSW index.
        */
       validateVector(vector) {
         if (vector.length !== this.config.dimensions) {
@@ -11598,6 +11611,33 @@ ${JSON.stringify(results.map((n61) => ({ id: n61.id, label: n61.label, propertie
   }
 });
 
+// src/shared/safe-db.ts
+var safe_db_exports = {};
+__export(safe_db_exports, {
+  openDatabase: () => openDatabase
+});
+function openDatabase(dbPath, opts) {
+  const readonly = opts?.readonly ?? false;
+  const fileMustExist = opts?.fileMustExist ?? false;
+  const busyTimeout = opts?.busyTimeout ?? 5e3;
+  const walMode = opts?.walMode ?? !readonly;
+  const db = new better_sqlite3_default(dbPath, {
+    readonly,
+    fileMustExist
+  });
+  db.pragma(`busy_timeout = ${busyTimeout}`);
+  if (walMode) {
+    db.pragma("journal_mode = WAL");
+  }
+  return db;
+}
+var init_safe_db = __esm({
+  "src/shared/safe-db.ts"() {
+    "use strict";
+    init_better_sqlite3();
+  }
+});
+
 // src/integrations/vibium/types.ts
 var init_types3 = __esm({
   "src/integrations/vibium/types.ts"() {
@@ -15066,7 +15106,7 @@ var logger9, V2ToV3Migrator;
 var init_v2_to_v3_migration = __esm({
   "src/learning/v2-to-v3-migration.ts"() {
     "use strict";
-    init_better_sqlite3();
+    init_safe_db();
     init_error_utils();
     init_safe_json();
     init_logging();
@@ -15168,9 +15208,8 @@ var init_v2_to_v3_migration = __esm({
         }
       }
       async connect() {
-        this.v2Db = new better_sqlite3_default(this.config.v2DbPath, { readonly: true });
-        this.v3Db = new better_sqlite3_default(this.config.v3PatternsDbPath);
-        this.v3Db.pragma("journal_mode = WAL");
+        this.v2Db = openDatabase(this.config.v2DbPath, { readonly: true });
+        this.v3Db = openDatabase(this.config.v3PatternsDbPath);
         this.createV3Schema();
       }
       async disconnect() {
@@ -15560,7 +15599,7 @@ var DEFAULT_SQLITE_CONFIG, SQLitePatternStore;
 var init_sqlite_persistence = __esm({
   "src/learning/sqlite-persistence.ts"() {
     "use strict";
-    init_better_sqlite3();
+    init_safe_db();
     init_esm_node();
     init_safe_json();
     init_error_utils();
@@ -15604,10 +15643,7 @@ var init_sqlite_persistence = __esm({
             if (!fs23.existsSync(dir)) {
               fs23.mkdirSync(dir, { recursive: true });
             }
-            this.db = new better_sqlite3_default(this.config.dbPath);
-            if (this.config.walMode) {
-              this.db.pragma("journal_mode = WAL");
-            }
+            this.db = openDatabase(this.config.dbPath);
             this.db.pragma(`mmap_size = ${this.config.mmapSize}`);
             this.db.pragma(`cache_size = ${this.config.cacheSize}`);
             if (this.config.foreignKeys) {
@@ -16782,11 +16818,11 @@ __export(hnswlib_node_exports, {
   init: () => init6,
   pipeline: () => pipeline7
 });
-import { createRequire as createRequire9 } from "module";
+import { createRequire as createRequire6 } from "module";
 var __require7, __mod6, hnswlib_node_default, RuvectorLayer6, TensorCompress6, differentiableSearch6, hierarchicalForward6, getCompressionLevel6, init6, FlashAttention6, DotProductAttention6, MultiHeadAttention6, HyperbolicAttention6, LinearAttention6, MoEAttention6, SonaEngine6, pipeline7;
 var init_hnswlib_node = __esm({
   "native-require:hnswlib-node"() {
-    __require7 = createRequire9(import.meta.url);
+    __require7 = createRequire6(import.meta.url);
     __mod6 = __require7("hnswlib-node");
     hnswlib_node_default = __mod6;
     ({
@@ -16839,11 +16875,11 @@ __export(pg_exports, {
   init: () => init7,
   pipeline: () => pipeline8
 });
-import { createRequire as createRequire10 } from "module";
+import { createRequire as createRequire7 } from "module";
 var __require8, __mod7, pg_default, RuvectorLayer7, TensorCompress7, differentiableSearch7, hierarchicalForward7, getCompressionLevel7, init7, FlashAttention7, DotProductAttention7, MultiHeadAttention7, HyperbolicAttention7, LinearAttention7, MoEAttention7, SonaEngine7, pipeline8;
 var init_pg = __esm({
   "native-require:pg"() {
-    __require8 = createRequire10(import.meta.url);
+    __require8 = createRequire7(import.meta.url);
     __mod7 = __require8("pg");
     pg_default = __mod7;
     ({
@@ -18294,11 +18330,11 @@ __export(prime_radiant_advanced_wasm_exports, {
   init: () => init8,
   pipeline: () => pipeline9
 });
-import { createRequire as createRequire11 } from "module";
+import { createRequire as createRequire8 } from "module";
 var __require9, __mod8, prime_radiant_advanced_wasm_default, RuvectorLayer8, TensorCompress8, differentiableSearch8, hierarchicalForward8, getCompressionLevel8, init8, FlashAttention8, DotProductAttention8, MultiHeadAttention8, HyperbolicAttention8, LinearAttention8, MoEAttention8, SonaEngine8, pipeline9;
 var init_prime_radiant_advanced_wasm = __esm({
   "native-require:prime-radiant-advanced-wasm"() {
-    __require9 = createRequire11(import.meta.url);
+    __require9 = createRequire8(import.meta.url);
     __mod8 = __require9("prime-radiant-advanced-wasm");
     prime_radiant_advanced_wasm_default = __mod8;
     ({
@@ -31486,8 +31522,8 @@ var DEFAULT_GOVERNANCE_FLAGS = {
   },
   shardEmbeddings: {
     enabled: true,
-    embeddingDimensions: 128,
-    // 128-dimensional embeddings
+    embeddingDimensions: 768,
+    // 768-dimensional embeddings (aligned with HNSW indices)
     persistEmbeddings: false,
     // Don't persist by default
     autoRebuildOnChange: true,
@@ -31608,7 +31644,7 @@ function loadFlagsFromEnv() {
     },
     shardEmbeddings: {
       enabled: env.GOVERNANCE_SHARD_EMBEDDINGS !== "false",
-      embeddingDimensions: parseInt(env.GOVERNANCE_EMBEDDING_DIMENSIONS || "128", 10),
+      embeddingDimensions: parseInt(env.GOVERNANCE_EMBEDDING_DIMENSIONS || "768", 10),
       persistEmbeddings: env.GOVERNANCE_PERSIST_EMBEDDINGS === "true",
       autoRebuildOnChange: env.GOVERNANCE_AUTO_REBUILD !== "false",
       ngramMin: parseInt(env.GOVERNANCE_NGRAM_MIN || "2", 10),
@@ -39107,7 +39143,7 @@ init_safe_json();
 init_unified_memory();
 var DEFAULT_SHARD_EMBEDDINGS_FLAGS = {
   enabled: true,
-  embeddingDimensions: 128,
+  embeddingDimensions: 768,
   persistEmbeddings: false,
   autoRebuildOnChange: true,
   ngramMin: 2,
@@ -41786,7 +41822,7 @@ var BaseRLAlgorithm = class {
 init_vector_math();
 var DEFAULT_DT_CONFIG = {
   contextLength: 10,
-  embeddingDim: 128,
+  embeddingDim: 768,
   numHeads: 4,
   numLayers: 3,
   feedForwardDim: 256,
@@ -42547,7 +42583,7 @@ var TestGenerationCoordinator = class extends BaseDomainCoordinator {
       try {
         this.decisionTransformer = new DecisionTransformerAlgorithm({
           contextLength: 10,
-          embeddingDim: 128
+          embeddingDim: 768
         });
         console.log("[TestGenerationCoordinator] DecisionTransformer created for test case selection");
       } catch (error) {
@@ -46391,7 +46427,7 @@ var DEFAULT_CONFIG10 = {
   enableAutoTraining: true,
   trainingInterval: 10,
   contextLength: 10,
-  embeddingDim: 128
+  embeddingDim: 768
 };
 var TestPrioritizerService = class {
   constructor(memory, config = {}) {
@@ -51734,7 +51770,7 @@ var DEFAULT_CONFIG11 = {
 };
 var CoverageAnalyzerService = class _CoverageAnalyzerService {
   static DEFAULT_THRESHOLD = 80;
-  static VECTOR_DIMENSION = 128;
+  static VECTOR_DIMENSION = 768;
   memory;
   config;
   llmRouter;
@@ -52268,7 +52304,7 @@ var DEFAULT_CONFIG12 = {
 };
 var GapDetectorService = class _GapDetectorService {
   static DEFAULT_MIN_COVERAGE = 80;
-  static VECTOR_DIMENSION = 128;
+  static VECTOR_DIMENSION = 768;
   memory;
   config;
   llmRouter;
@@ -53266,7 +53302,7 @@ init_hnsw_index();
 
 // src/domains/coverage-analysis/services/coverage-embedder.ts
 var DEFAULT_EMBEDDER_CONFIG = {
-  dimensions: 128,
+  dimensions: 768,
   includePathFeatures: true,
   includeTemporalFeatures: true,
   normalization: "l2"
@@ -53698,7 +53734,7 @@ var ALL_CATEGORIES = [
   "missing-security-check"
 ];
 var DEFAULT_CONFIG13 = {
-  dimensions: 128,
+  dimensions: 768,
   minConfidence: 0.3,
   maxGaps: 50,
   riskWeight: 0.6,
@@ -55407,7 +55443,7 @@ var CoverageAnalysisCoordinator = class extends BaseDomainCoordinator {
     return forecast;
   }
   createGapEmbedding(gap) {
-    const VECTOR_DIMENSION = 128;
+    const VECTOR_DIMENSION = 768;
     const embedding = new Array(VECTOR_DIMENSION).fill(0);
     embedding[0] = gap.riskScore;
     embedding[1] = Math.min(1, gap.lines.length / 100);
@@ -73262,7 +73298,7 @@ var CodeIntelligenceCoordinator = class extends BaseDomainCoordinator {
    */
   async initializeHypergraph() {
     try {
-      const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
+      const { openDatabase: openDatabase2 } = await Promise.resolve().then(() => (init_safe_db(), safe_db_exports));
       const fs23 = await import("fs");
       const path26 = await import("path");
       const { findProjectRoot: findProjectRoot2 } = await Promise.resolve().then(() => (init_unified_memory(), unified_memory_exports));
@@ -73272,7 +73308,7 @@ var CodeIntelligenceCoordinator = class extends BaseDomainCoordinator {
       if (!fs23.existsSync(dir)) {
         fs23.mkdirSync(dir, { recursive: true });
       }
-      this.hypergraphDb = new Database(dbPath);
+      this.hypergraphDb = openDatabase2(dbPath);
       this.hypergraph = await createHypergraphEngine({
         db: this.hypergraphDb,
         maxTraversalDepth: 10,
@@ -74884,6 +74920,18 @@ var SECRET_PATTERNS = [
     owaspId: "A02:2021",
     cweId: "CWE-798",
     remediation: "Use environment variables for Slack tokens"
+  },
+  {
+    id: "secret-generic-assignment",
+    pattern: /\b\w*(?:SECRET|secret)(?:_KEY|_key|Key)?\s*[:=]\s*['"`][^'"`]{4,}['"`]/g,
+    category: "sensitive-data",
+    severity: "high",
+    title: "Generic Secret Assignment Detected",
+    description: "Hardcoded secret assignment (SECRET_KEY, JWT_SECRET, APP_SECRET, etc.) found in source code",
+    owaspId: "A02:2021",
+    cweId: "CWE-798",
+    remediation: "Use environment variables or a secrets manager instead of hardcoding secrets",
+    fixExample: "const secretKey = process.env.SECRET_KEY"
   }
 ];
 var PATH_TRAVERSAL_PATTERNS2 = [
@@ -115401,7 +115449,7 @@ var ALL_DOMAINS2 = [
   "enterprise-integration"
 ];
 function getAQEVersion() {
-  return true ? "3.6.11" : "3.0.0";
+  return true ? "3.6.13" : "3.0.0";
 }
 function createDefaultConfig(projectName, projectRoot) {
   return {
@@ -116307,14 +116355,12 @@ function createSelfConfigurator(options) {
 // src/init/init-wizard-migration.ts
 import { existsSync as existsSync15, mkdirSync as mkdirSync5, writeFileSync as writeFileSync2, readFileSync as readFileSync12, readdirSync as readdirSync5, statSync as statSync5, unlinkSync as unlinkSync2, copyFileSync as copyFileSync2 } from "fs";
 import { join as join17, dirname as dirname4 } from "path";
-import { createRequire as createRequire6 } from "module";
 init_error_utils();
 init_safe_json();
-var require2 = createRequire6(import.meta.url);
+init_safe_db();
 function readVersionFromDb(dbPath) {
   try {
-    const Database = require2("better-sqlite3");
-    const db = new Database(dbPath, { readonly: true, fileMustExist: true });
+    const db = openDatabase(dbPath, { readonly: true, fileMustExist: true });
     try {
       const tableExists = db.prepare(`
         SELECT name FROM sqlite_master
@@ -116348,8 +116394,7 @@ async function writeVersionToDb(projectRoot, version) {
     if (!existsSync15(dir)) {
       mkdirSync5(dir, { recursive: true });
     }
-    const Database = require2("better-sqlite3");
-    const db = new Database(memoryDbPath);
+    const db = openDatabase(memoryDbPath);
     try {
       db.exec(`
         CREATE TABLE IF NOT EXISTS kv_store (
@@ -118477,6 +118522,7 @@ function createN8nInstaller(options) {
 
 // src/init/init-wizard-steps.ts
 init_error_utils();
+init_safe_db();
 async function initializePersistenceDatabase(projectRoot) {
   let Database = null;
   try {
@@ -118536,8 +118582,7 @@ async function checkCodeIntelligenceIndex(projectRoot) {
     return false;
   }
   try {
-    const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-    const db = new Database(dbPath);
+    const db = openDatabase(dbPath);
     const result = db.prepare(`
       SELECT COUNT(*) as count FROM kv_store
       WHERE namespace = 'code-intelligence:kg'
@@ -118590,8 +118635,7 @@ async function runCodeIntelligenceScan(projectPath) {
 async function getKGEntryCount(projectRoot) {
   const dbPath = join22(projectRoot, ".agentic-qe", "memory.db");
   try {
-    const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-    const db = new Database(dbPath);
+    const db = openDatabase(dbPath);
     const result = db.prepare(`
       SELECT COUNT(*) as count FROM kv_store
       WHERE namespace LIKE 'code-intelligence:kg%'
@@ -119266,10 +119310,9 @@ var BasePhase = class {
 
 // src/init/phases/01-detection.ts
 init_safe_json();
+init_safe_db();
 import { existsSync as existsSync21 } from "fs";
 import { join as join23 } from "path";
-import { createRequire as createRequire7 } from "module";
-var require3 = createRequire7(import.meta.url);
 var DetectionPhase = class extends BasePhase {
   name = "detection";
   description = "Detect existing installations";
@@ -119358,8 +119401,7 @@ var DetectionPhase = class extends BasePhase {
    */
   readVersionFromDb(dbPath) {
     try {
-      const Database = require3("better-sqlite3");
-      const db = new Database(dbPath, { readonly: true, fileMustExist: true });
+      const db = openDatabase(dbPath, { readonly: true, fileMustExist: true });
       try {
         const tableExists = db.prepare(`
           SELECT name FROM sqlite_master
@@ -119629,6 +119671,7 @@ var LearningPhase = class extends BasePhase {
 
 // src/init/phases/06-code-intelligence.ts
 init_safe_json();
+init_safe_db();
 import { existsSync as existsSync24, statSync as statSync8 } from "fs";
 import { join as join26 } from "path";
 var SCAN_IGNORE_PATTERNS = [
@@ -119698,8 +119741,7 @@ var CodeIntelligencePhase = class extends BasePhase {
       return false;
     }
     try {
-      const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-      const db = new Database(dbPath);
+      const db = openDatabase(dbPath);
       const result = db.prepare(`
         SELECT COUNT(*) as count FROM kv_store
         WHERE namespace = 'code-intelligence:kg'
@@ -119716,8 +119758,7 @@ var CodeIntelligencePhase = class extends BasePhase {
   async getKGEntryCount(projectRoot) {
     const dbPath = join26(projectRoot, ".agentic-qe", "memory.db");
     try {
-      const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-      const db = new Database(dbPath);
+      const db = openDatabase(dbPath);
       const result = db.prepare(`
         SELECT COUNT(*) as count FROM kv_store
         WHERE namespace LIKE 'code-intelligence:kg%'
@@ -119796,8 +119837,7 @@ var CodeIntelligencePhase = class extends BasePhase {
   async getLastIndexedAt(projectRoot) {
     const dbPath = join26(projectRoot, ".agentic-qe", "memory.db");
     try {
-      const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-      const db = new Database(dbPath);
+      const db = openDatabase(dbPath);
       const row = db.prepare(`
         SELECT value FROM kv_store
         WHERE namespace = 'code-intelligence:kg'
@@ -119872,6 +119912,10 @@ var HooksPhase = class extends BasePhase {
     if (!existsSync25(claudeDir)) {
       mkdirSync13(claudeDir, { recursive: true });
     }
+    const hooksDir = join27(claudeDir, "hooks");
+    if (!existsSync25(hooksDir)) {
+      mkdirSync13(hooksDir, { recursive: true });
+    }
     const settingsPath = join27(claudeDir, "settings.json");
     let settings = {};
     if (existsSync25(settingsPath)) {
@@ -119906,7 +119950,20 @@ var HooksPhase = class extends BasePhase {
     }
     settings.enabledMcpjsonServers = existingMcp;
     writeFileSync9(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
+    this.writeHooksReadme(hooksDir, hookTypes);
+    this.installHookAssets(hooksDir, context2);
+    try {
+      const verifyContent = readFileSync17(settingsPath, "utf-8");
+      const verifySettings = safeJsonParse(verifyContent);
+      const verifyHooks = verifySettings.hooks;
+      if (!verifyHooks || !this.hasExistingAqeHooks(verifyHooks)) {
+        context2.services.log("  WARNING: settings.json written but AQE hooks not detected \u2014 check settings-merge logic");
+      }
+    } catch {
+      context2.services.log("  WARNING: Could not verify settings.json after write");
+    }
     context2.services.log(`  Settings: ${settingsPath}`);
+    context2.services.log(`  Hooks dir: ${hooksDir}`);
     context2.services.log(`  Hook types: ${hookTypes.join(", ")}`);
     return {
       configured: true,
@@ -119915,6 +119972,83 @@ var HooksPhase = class extends BasePhase {
       existingAqeDetected
     };
   }
+  /**
+   * Write a README to .claude/hooks/ explaining the hook setup.
+   * Actual hook config lives in .claude/settings.json (Claude Code reads it from there).
+   * The hooks dir contains supporting infrastructure (bridge script, workers config).
+   */
+  writeHooksReadme(hooksDir, hookTypes) {
+    const readmePath = join27(hooksDir, "README.txt");
+    if (existsSync25(readmePath)) return;
+    const content = [
+      "AQE Hooks Directory",
+      "====================",
+      "",
+      "Claude Code hooks are configured in .claude/settings.json (not as files here).",
+      "This directory contains supporting infrastructure for the learning system.",
+      "",
+      "Configured hook types: " + hookTypes.join(", "),
+      "",
+      "Files:",
+      "  settings.json  \u2014 Hook definitions (in parent .claude/ directory)",
+      "  v3-qe-bridge.sh \u2014 Bridge script connecting Claude Code events to QE learning",
+      "  v3-domain-workers.json \u2014 Domain worker configuration",
+      "  cross-phase-memory.yaml \u2014 QCSD feedback loop configuration",
+      "",
+      "Manual testing:",
+      "  npx agentic-qe hooks session-start --session-id test --json",
+      '  npx agentic-qe hooks route --task "generate tests" --json',
+      "  npx agentic-qe hooks post-edit --file src/example.ts --success --json",
+      ""
+    ].join("\n");
+    writeFileSync9(readmePath, content, "utf-8");
+  }
+  /**
+   * Install hook assets (cross-phase memory config, domain workers).
+   * Copies from v3/assets/hooks/ if available, otherwise creates minimal defaults.
+   */
+  installHookAssets(hooksDir, context2) {
+    const { projectRoot } = context2;
+    const crossPhasePath = join27(hooksDir, "cross-phase-memory.yaml");
+    if (!existsSync25(crossPhasePath)) {
+      const assetPaths = [
+        join27(projectRoot, "v3", "assets", "hooks", "cross-phase-memory.yaml"),
+        join27(projectRoot, "assets", "hooks", "cross-phase-memory.yaml"),
+        join27(projectRoot, "node_modules", "agentic-qe", "v3", "assets", "hooks", "cross-phase-memory.yaml")
+      ];
+      let installed = false;
+      for (const src of assetPaths) {
+        if (existsSync25(src)) {
+          const { copyFileSync: copyFileSync9 } = __require("fs");
+          copyFileSync9(src, crossPhasePath);
+          context2.services.log("  Installed cross-phase memory config");
+          installed = true;
+          break;
+        }
+      }
+      if (!installed) {
+        writeFileSync9(crossPhasePath, [
+          "# Cross-Phase Memory Hooks Configuration",
+          "# Generated by aqe init",
+          'version: "1.0"',
+          "enabled: true",
+          ""
+        ].join("\n"), "utf-8");
+      }
+    }
+    const workersPath = join27(hooksDir, "v3-domain-workers.json");
+    if (!existsSync25(workersPath)) {
+      writeFileSync9(workersPath, JSON.stringify({
+        version: "3.0",
+        workers: [
+          { name: "pattern-consolidator", interval: "5m", enabled: true },
+          { name: "routing-accuracy-monitor", interval: "10m", enabled: true },
+          { name: "coverage-gap-scanner", interval: "15m", enabled: true },
+          { name: "flaky-test-detector", interval: "30m", enabled: true }
+        ]
+      }, null, 2), "utf-8");
+    }
+  }
   /**
    * Check if existing hooks contain any AQE/agentic-qe entries
    */
@@ -120770,8 +120904,7 @@ Task({ prompt: "Security audit", subagent_type: "qe-security-scanner", run_in_ba
 import { existsSync as existsSync30, readFileSync as readFileSync22 } from "fs";
 import { join as join32, dirname as dirname9 } from "path";
 import { mkdirSync as mkdirSync16, writeFileSync as writeFileSync13 } from "fs";
-import { createRequire as createRequire8 } from "module";
-var require4 = createRequire8(import.meta.url);
+init_safe_db();
 var VerificationPhase = class extends BasePhase {
   name = "verification";
   description = "Verify installation";
@@ -120828,8 +120961,7 @@ var VerificationPhase = class extends BasePhase {
       if (!existsSync30(dir)) {
         mkdirSync16(dir, { recursive: true });
       }
-      const Database = require4("better-sqlite3");
-      const db = new Database(memoryDbPath);
+      const db = openDatabase(memoryDbPath);
       try {
         db.exec(`
           CREATE TABLE IF NOT EXISTS kv_store (
@@ -125002,7 +125134,7 @@ function createMigrateCommand(context2, cleanupAndExit2, ensureInitialized2) {
           migratedFrom: "v2",
           migratedAt: (/* @__PURE__ */ new Date()).toISOString(),
           hnswEnabled: true,
-          vectorDimensions: 128
+          vectorDimensions: 768
         }, null, 2));
         const stats = fs23.statSync(v2Files.memoryDb);
         console.log(chalk17.green(`   * Memory database migrated (${(stats.size / 1024).toFixed(1)} KB)
@@ -125031,7 +125163,7 @@ function createMigrateCommand(context2, cleanupAndExit2, ensureInitialized2) {
           domains: {
             "test-generation": { enabled: true },
             "test-execution": { enabled: true },
-            "coverage-analysis": { enabled: true, algorithm: "hnsw", dimensions: 128 },
+            "coverage-analysis": { enabled: true, algorithm: "hnsw", dimensions: 768 },
             "quality-assessment": { enabled: true },
             "defect-intelligence": { enabled: true },
             "requirements-validation": { enabled: true },
@@ -126972,6 +127104,7 @@ import chalk20 from "chalk";
 
 // src/init/fleet-integration.ts
 init_error_utils();
+init_safe_db();
 import chalk19 from "chalk";
 import { existsSync as existsSync38 } from "fs";
 import { join as join40 } from "path";
@@ -127126,8 +127259,7 @@ var FleetInitEnhancer = class {
       return false;
     }
     try {
-      const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-      const db = new Database(dbPath);
+      const db = openDatabase(dbPath);
       const result = db.prepare(`
         SELECT COUNT(*) as count FROM kv_store
         WHERE namespace = 'code-intelligence:kg'
@@ -127144,8 +127276,7 @@ var FleetInitEnhancer = class {
   async getKGEntryCount() {
     const dbPath = join40(this.projectRoot, ".agentic-qe", "memory.db");
     try {
-      const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-      const db = new Database(dbPath);
+      const db = openDatabase(dbPath);
       const result = db.prepare(`
         SELECT COUNT(*) as count FROM kv_store
         WHERE namespace LIKE 'code-intelligence:kg%'
@@ -132580,7 +132711,7 @@ var DEFAULT_SYNC_CONFIG = {
 };
 
 // src/sync/readers/sqlite-reader.ts
-init_better_sqlite3();
+init_safe_db();
 init_sql_safety();
 init_safe_json();
 init_error_utils();
@@ -132608,7 +132739,7 @@ var SQLiteReader = class {
       throw new Error(`SQLite database not found: ${this.dbPath}`);
     }
     try {
-      this.db = new better_sqlite3_default(this.dbPath, { readonly: true });
+      this.db = openDatabase(this.dbPath, { readonly: true });
       this.db.pragma("journal_mode = WAL");
       this.db.pragma("synchronous = NORMAL");
       console.log(`[SQLiteReader:${this.name}] Initialized: ${this.dbPath}`);
@@ -133974,7 +134105,7 @@ async function syncIncrementalToCloud(since, config) {
 }
 
 // src/integrations/embeddings/cache/EmbeddingCache.ts
-init_better_sqlite3();
+init_safe_db();
 init_unified_memory();
 init_safe_json();
 
@@ -133983,7 +134114,7 @@ init_transformers();
 init_vector_math();
 
 // src/sync/embeddings/sync-embedding-generator.ts
-init_better_sqlite3();
+init_safe_db();
 init_sql_safety();
 init_error_utils();
 init_safe_json();
@@ -136938,7 +137069,7 @@ async function createCoherenceService(wasmLoader2, config, logger19) {
 
 // src/integrations/coherence/wasm-loader.ts
 init_error_utils();
-import { createRequire as createRequire12 } from "node:module";
+import { createRequire as createRequire9 } from "node:module";
 import { fileURLToPath as fileURLToPath6 } from "node:url";
 import { dirname as dirname13, join as join44 } from "node:path";
 import { readFileSync as readFileSync32, existsSync as existsSync44 } from "node:fs";
@@ -137194,11 +137325,11 @@ var WasmLoader = class {
       return false;
     }
     try {
-      const require5 = createRequire12(import.meta.url);
+      const require2 = createRequire9(import.meta.url);
       const wasmPaths = [
         (() => {
           try {
-            const modulePath = require5.resolve("prime-radiant-advanced-wasm");
+            const modulePath = require2.resolve("prime-radiant-advanced-wasm");
             return join44(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
           } catch {
             return null;
@@ -137400,18 +137531,18 @@ var WasmLoader = class {
    * - Browser: Uses default() async init with fetch
    */
   async attemptLoad() {
-    let require5;
+    let require2;
     try {
-      require5 = createRequire12(import.meta.url);
+      require2 = createRequire9(import.meta.url);
     } catch {
-      require5 = globalThis.require || (await import("module")).createRequire(__filename);
+      require2 = globalThis.require || (await import("module")).createRequire(__filename);
     }
     let wasmModule;
     try {
       wasmModule = await Promise.resolve().then(() => (init_prime_radiant_advanced_wasm(), prime_radiant_advanced_wasm_exports));
     } catch (importError) {
       try {
-        wasmModule = require5("prime-radiant-advanced-wasm");
+        wasmModule = require2("prime-radiant-advanced-wasm");
       } catch (requireError) {
         throw new Error(
           `Failed to import prime-radiant-advanced-wasm: ${toErrorMessage(importError)}`
@@ -137420,7 +137551,7 @@ var WasmLoader = class {
     }
     const isNodeJs = typeof process !== "undefined" && process.versions != null && process.versions.node != null;
     if (isNodeJs) {
-      await this.initializeForNodeJs(wasmModule, require5);
+      await this.initializeForNodeJs(wasmModule, require2);
     } else {
       if (wasmModule.default && typeof wasmModule.default === "function") {
         await wasmModule.default();
@@ -137452,12 +137583,12 @@ var WasmLoader = class {
    * In Node.js, the default async init uses fetch() which isn't available.
    * Instead, we read the WASM binary from disk and use initSync().
    */
-  async initializeForNodeJs(wasmModule, require5) {
+  async initializeForNodeJs(wasmModule, require2) {
     const wasmPaths = [
       // Resolve from require - most reliable
       (() => {
         try {
-          const modulePath = require5.resolve("prime-radiant-advanced-wasm");
+          const modulePath = require2.resolve("prime-radiant-advanced-wasm");
           return join44(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
         } catch {
           return null;
@@ -138684,7 +138815,7 @@ import { existsSync as existsSync46, writeFileSync as writeFileSync22, readFileS
 import { stat as stat3, unlink } from "node:fs/promises";
 
 // src/learning/metrics-tracker.ts
-init_better_sqlite3();
+init_safe_db();
 init_qe_patterns();
 init_safe_json();
 init_logging();
@@ -138706,7 +138837,7 @@ var LearningMetricsTracker = class {
     if (!existsSync45(this.dbPath)) {
       throw new Error(`Database not found: ${this.dbPath}. Run "aqe init --auto" first.`);
     }
-    this.db = new better_sqlite3_default(this.dbPath, { readonly: false });
+    this.db = openDatabase(this.dbPath);
     this.ensureMetricsTable();
     this.initialized = true;
   }
@@ -139054,9 +139185,13 @@ function createLearningMetricsTracker(projectRoot) {
   return new LearningMetricsTracker(projectRoot);
 }
 
+// src/cli/commands/learning.ts
+init_safe_db();
+
 // src/cli/commands/learning-helpers.ts
 init_unified_memory();
 init_qe_reasoning_bank();
+init_safe_db();
 import chalk28 from "chalk";
 import path24 from "node:path";
 import { createReadStream, createWriteStream } from "node:fs";
@@ -139205,8 +139340,7 @@ async function decompressFile(gzPath, outputPath) {
 }
 async function verifyDatabaseIntegrity(dbPath) {
   try {
-    const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-    const db = new Database(dbPath, { readonly: true });
+    const db = openDatabase(dbPath, { readonly: true });
     const result = db.prepare("PRAGMA integrity_check").get();
     db.close();
     if (result.integrity_check === "ok") {
@@ -139223,8 +139357,7 @@ async function verifyDatabaseIntegrity(dbPath) {
 }
 async function getSchemaVersion(dbPath) {
   try {
-    const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-    const db = new Database(dbPath, { readonly: true });
+    const db = openDatabase(dbPath, { readonly: true });
     const tableExists = db.prepare(
       "SELECT name FROM sqlite_master WHERE type='table' AND name='schema_version'"
     ).get();
@@ -139583,8 +139716,7 @@ function registerExtractCommand(learning) {
       console.log(`  Min reward threshold: ${minReward}`);
       console.log(`  Min occurrences: ${minCount}
 `);
-      const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-      const db = new Database(dbPath, { readonly: true });
+      const db = openDatabase(dbPath, { readonly: true });
       const experiences = db.prepare(`
           SELECT task_type, COUNT(*) as count, AVG(reward) as avg_reward, MAX(reward) as max_reward,
                  MIN(reward) as min_reward, GROUP_CONCAT(DISTINCT action) as actions
@@ -139840,8 +139972,7 @@ function registerVerifyCommand(learning) {
       const fileStats = await stat3(dbPath);
       let tableCounts = {};
       try {
-        const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-        const db = new Database(dbPath, { readonly: true });
+        const db = openDatabase(dbPath, { readonly: true });
         for (const table of ["qe_patterns", "qe_trajectories", "learning_experiences", "kv_store", "vectors"]) {
           try {
             const r54 = db.prepare(`SELECT COUNT(*) as count FROM ${table}`).get();
@@ -139908,8 +140039,7 @@ function registerExportFullCommand(learning) {
       };
       if (options.includeTrajectories) {
         try {
-          const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-          const db = new Database(dbPath, { readonly: true });
+          const db = openDatabase(dbPath, { readonly: true });
           const trajectories = db.prepare(`SELECT id, task, agent, domain, success, steps_json FROM qe_trajectories ORDER BY started_at DESC LIMIT 1000`).all();
           exportData.trajectories = trajectories.map((t50) => ({ id: t50.id, task: t50.task, agent: t50.agent, domain: t50.domain, success: t50.success, stepsJson: t50.steps_json }));
           db.close();
@@ -139918,8 +140048,7 @@ function registerExportFullCommand(learning) {
       }
       if (options.includeExperiences) {
         try {
-          const Database = (await Promise.resolve().then(() => (init_better_sqlite3(), better_sqlite3_exports))).default;
-          const db = new Database(dbPath, { readonly: true });
+          const db = openDatabase(dbPath, { readonly: true });
           const experiences = db.prepare(`SELECT task_type, action, AVG(reward) as avg_reward, COUNT(*) as count FROM learning_experiences GROUP BY task_type, action ORDER BY count DESC LIMIT 500`).all();
           exportData.experiences = experiences.map((e20) => ({ taskType: e20.task_type, action: e20.action, reward: e20.avg_reward, count: e20.count }));
           const metaRow = db.prepare(`SELECT COUNT(*) as total, AVG(reward) as avg_reward FROM learning_experiences`).get();
@@ -140415,7 +140544,7 @@ async function cleanupAndExit(code = 0) {
   process.exit(code);
 }
 var program = new Command18();
-var VERSION = true ? "3.6.11" : "0.0.0-dev";
+var VERSION = true ? "3.6.13" : "0.0.0-dev";
 program.name("aqe").description("Agentic QE - Domain-Driven Quality Engineering").version(VERSION);
 var registry = createCommandRegistry(context, cleanupAndExit, ensureInitialized);
 registry.registerAll(program);