agentic-qe 3.6.10 → 3.6.12

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,
@@ -8841,7 +8854,7 @@ var init_hnsw_index = __esm({
         if (!this.initialized) {
           await this.initialize();
         }
-        this.validateVector(vector);
+        vector = this.validateVector(vector);
         if (this.keyToLabel.has(key)) {
           await this.delete(key);
         }
@@ -8870,7 +8883,7 @@ var init_hnsw_index = __esm({
         if (!this.initialized) {
           await this.initialize();
         }
-        this.validateVector(query);
+        query = this.validateVector(query);
         const startTime = performance.now();
         const results = this.stats.vectorCount > 0 ? this.searchRuvector(query, k68) : [];
         const endTime = performance.now();
@@ -8995,17 +9008,46 @@ var init_hnsw_index = __esm({
       // ============================================================================
       // Private Helper Methods
       // ============================================================================
+      /**
+       * Validate and auto-resize vectors to match HNSW configured dimensions.
+       * Fix #279: Prevents Rust WASM panic when RealEmbeddings (768-dim) are
+       * passed to a mismatched-dim HNSW index.
+       */
       validateVector(vector) {
         if (vector.length !== this.config.dimensions) {
-          throw new Error(
-            `Vector dimension mismatch: expected ${this.config.dimensions}, got ${vector.length}`
-          );
+          return this.resizeVector(vector, this.config.dimensions);
         }
         for (let i58 = 0; i58 < vector.length; i58++) {
           if (!Number.isFinite(vector[i58])) {
             throw new Error(`Invalid vector value at index ${i58}: ${vector[i58]}`);
           }
         }
+        return vector;
+      }
+      /**
+       * Resize vector to target dimensions using averaging (shrink) or zero-padding (grow).
+       */
+      resizeVector(vector, targetDim) {
+        if (vector.length === targetDim) return vector;
+        if (vector.length > targetDim) {
+          const result2 = new Array(targetDim).fill(0);
+          const ratio = vector.length / targetDim;
+          for (let i58 = 0; i58 < targetDim; i58++) {
+            const start = Math.floor(i58 * ratio);
+            const end = Math.floor((i58 + 1) * ratio);
+            let sum = 0;
+            for (let j52 = start; j52 < end; j52++) {
+              sum += vector[j52];
+            }
+            result2[i58] = sum / (end - start);
+          }
+          return result2;
+        }
+        const result = new Array(targetDim).fill(0);
+        for (let i58 = 0; i58 < vector.length; i58++) {
+          result[i58] = vector[i58];
+        }
+        return result;
       }
       buildKey(key) {
         return `${this.config.namespace}:${key}`;
@@ -11569,6 +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"() {
@@ -15037,7 +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();
@@ -15139,9 +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() {
@@ -15531,7 +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();
@@ -15575,10 +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) {
@@ -16753,11 +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;
     ({
@@ -16810,11 +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;
     ({
@@ -18265,11 +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;
     ({
@@ -51705,7 +51770,7 @@ var DEFAULT_CONFIG11 = {
 };
 var CoverageAnalyzerService = class _CoverageAnalyzerService {
   static DEFAULT_THRESHOLD = 80;
-  static VECTOR_DIMENSION = 128;
+  static VECTOR_DIMENSION = 768;
   memory;
   config;
   llmRouter;
@@ -52239,7 +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;
@@ -53237,7 +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"
@@ -53669,7 +53734,7 @@ var ALL_CATEGORIES = [
   "missing-security-check"
 ];
 var DEFAULT_CONFIG13 = {
-  dimensions: 128,
+  dimensions: 768,
   minConfidence: 0.3,
   maxGaps: 50,
   riskWeight: 0.6,
@@ -55378,7 +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);
@@ -70816,7 +70881,35 @@ import { join as join10, extname as extname3 } from "path";
 // src/domains/code-intelligence/services/metric-collector/interfaces.ts
 var DEFAULT_METRIC_CONFIG = {
   timeout: 6e4,
-  excludeDirs: ["node_modules", "dist", "coverage", "build", ".git", "vendor", "target"],
+  excludeDirs: [
+    // JS/TS ecosystem
+    "node_modules",
+    "dist",
+    "build",
+    "coverage",
+    ".nyc_output",
+    ".next",
+    ".nuxt",
+    ".output",
+    // Python ecosystem
+    "__pycache__",
+    ".venv",
+    "venv",
+    ".tox",
+    ".mypy_cache",
+    ".pytest_cache",
+    ".eggs",
+    "*.egg-info",
+    // Rust / Java / Go
+    "target",
+    ".gradle",
+    "vendor",
+    ".bundle",
+    // General
+    ".git",
+    ".svn",
+    ".hg"
+  ],
   testPatterns: ["**/*.test.ts", "**/*.spec.ts", "**/*.test.js", "**/*.spec.js"],
   enableCache: true,
   cacheTTL: 3e5
@@ -70824,7 +70917,7 @@ var DEFAULT_METRIC_CONFIG = {
 
 // src/domains/code-intelligence/services/metric-collector/loc-counter.ts
 import { execSync as execSync3, spawnSync as spawnSync2 } from "child_process";
-import { existsSync as existsSync6, readdirSync, readFileSync as readFileSync5 } from "fs";
+import { existsSync as existsSync6, readdirSync, readFileSync as readFileSync5, statSync as statSync2 } from "fs";
 import { join as join8, extname } from "path";
 init_safe_json();
 async function countLOC(projectPath, config = {}) {
@@ -70968,22 +71061,35 @@ function getLanguageForExtension(ext) {
 function manualLOCCount(projectPath, config) {
   const byLanguage = {};
   let total = 0;
-  function walkDirectory3(dirPath) {
-    if (!existsSync6(dirPath)) {
+  const excludeSet = new Set(config.excludeDirs);
+  const MAX_FILE_SIZE = 2 * 1024 * 1024;
+  function walkDirectory3(dirPath, depth) {
+    if (!existsSync6(dirPath) || depth > 20) {
+      return;
+    }
+    let entries;
+    try {
+      entries = readdirSync(dirPath, { withFileTypes: true });
+    } catch {
       return;
     }
-    const entries = readdirSync(dirPath, { withFileTypes: true });
     for (const entry of entries) {
       const fullPath = join8(dirPath, entry.name);
       if (entry.isDirectory()) {
-        if (config.excludeDirs.includes(entry.name)) {
+        if (excludeSet.has(entry.name) || entry.name.startsWith(".")) {
           continue;
         }
-        walkDirectory3(fullPath);
+        walkDirectory3(fullPath, depth + 1);
       } else if (entry.isFile()) {
         const ext = extname(entry.name);
         const language = getLanguageForExtension(ext);
         if (language) {
+          try {
+            const stat4 = statSync2(fullPath);
+            if (stat4.size > MAX_FILE_SIZE) continue;
+          } catch {
+            continue;
+          }
           const lines = countFileLines(fullPath);
           byLanguage[language] = (byLanguage[language] || 0) + lines;
           total += lines;
@@ -70991,11 +71097,11 @@ function manualLOCCount(projectPath, config) {
       }
     }
   }
-  walkDirectory3(projectPath);
+  walkDirectory3(projectPath, 0);
   return {
     total,
     byLanguage,
-    source: "fallback",
+    source: "node-native",
     excludedDirs: config.excludeDirs
   };
 }
@@ -71626,12 +71732,19 @@ var MetricCollectorService = class {
     const toolsUsed = [];
     if (loc.source !== "fallback") toolsUsed.push(loc.source);
     if (tests.source !== "fallback") toolsUsed.push(tests.source);
+    const locAccuracy = loc.source === "fallback" ? "approximate" : "accurate";
+    const testAccuracy = tests.source === "fallback" ? "approximate" : "accurate";
     const metrics = {
       loc,
       tests,
       patterns,
       collectedAt: /* @__PURE__ */ new Date(),
-      toolsUsed
+      toolsUsed,
+      accuracy: {
+        loc: locAccuracy,
+        tests: testAccuracy,
+        overall: locAccuracy === "accurate" && testAccuracy === "accurate" ? "accurate" : "approximate"
+      }
     };
     if (this.config.enableCache) {
       this.setInCache(cacheKey, metrics);
@@ -73185,7 +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));
@@ -73195,7 +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,
@@ -73861,9 +73974,15 @@ var CodeIntelligenceCoordinator = class extends BaseDomainCoordinator {
     try {
       console.log(`[CodeIntelligence] Collecting real metrics for ${projectPath}`);
       const metrics = await this.metricCollector.collectAll(projectPath);
+      const toolsLabel = metrics.toolsUsed.length > 0 ? metrics.toolsUsed.join(", ") : metrics.loc.source === "node-native" ? "node-native" : "fallback";
       console.log(
-        `[CodeIntelligence] Real metrics collected: ${metrics.loc.total} LOC, ${metrics.tests.total} tests, tools: ${metrics.toolsUsed.join(", ") || "fallback"}`
+        `[CodeIntelligence] Real metrics collected: ${metrics.loc.total} LOC, ${metrics.tests.total} tests, tools: ${toolsLabel}`
       );
+      if (metrics.loc.source === "node-native") {
+        console.log(
+          `[CodeIntelligence] Using Node.js-native line counter (no cloc/tokei needed)`
+        );
+      }
       await this.storeProjectMetricsInMemory(projectPath, metrics);
       if (this.config.publishEvents) {
         const event = createEvent(
@@ -115318,7 +115437,7 @@ var ALL_DOMAINS2 = [
   "enterprise-integration"
 ];
 function getAQEVersion() {
-  return true ? "3.6.10" : "3.0.0";
+  return true ? "3.6.12" : "3.0.0";
 }
 function createDefaultConfig(projectName, projectRoot) {
   return {
@@ -116224,14 +116343,12 @@ 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
@@ -116265,8 +116382,7 @@ 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 (
@@ -116525,6 +116641,110 @@ function readJsonSafe(filePath) {
 init_safe_json();
 import { existsSync as existsSync16, mkdirSync as mkdirSync6, writeFileSync as writeFileSync3, readFileSync as readFileSync13, copyFileSync as copyFileSync3 } from "fs";
 import { join as join18, dirname as dirname5 } from "path";
+
+// src/init/settings-merge.ts
+var AQE_COMMAND_PATTERNS = [
+  /\baqe\b/i,
+  /\bagentic-qe\b/i,
+  /\bnpx\s+agentic-qe\b/i,
+  /\bnpx\s+@anthropics\/agentic-qe\b/i
+];
+function isAqeHookEntry(entry) {
+  const hookEntry = entry;
+  if (!hookEntry?.hooks || !Array.isArray(hookEntry.hooks)) return false;
+  return hookEntry.hooks.some((h66) => {
+    if (!h66.command || typeof h66.command !== "string") return false;
+    return AQE_COMMAND_PATTERNS.some((pattern) => pattern.test(h66.command));
+  });
+}
+function mergeHooksSmart(existingHooks, newAqeHooks) {
+  const merged = {};
+  for (const [hookType, newEntries] of Object.entries(newAqeHooks)) {
+    const existing = existingHooks[hookType] || [];
+    const userEntries = Array.isArray(existing) ? existing.filter((entry) => !isAqeHookEntry(entry)) : [];
+    merged[hookType] = [...newEntries, ...userEntries];
+  }
+  for (const [hookType, hookArray] of Object.entries(existingHooks)) {
+    if (!merged[hookType]) {
+      merged[hookType] = hookArray;
+    }
+  }
+  return merged;
+}
+function generateAqeEnvVars(config) {
+  const domains = config.domains?.enabled || [];
+  return {
+    AQE_MEMORY_PATH: ".agentic-qe/memory.db",
+    AQE_MEMORY_ENABLED: "true",
+    AQE_LEARNING_ENABLED: config.learning?.enabled ? "true" : "false",
+    AQE_V3_MODE: "true",
+    AQE_V3_DDD_ENABLED: "true",
+    AQE_V3_DOMAINS: domains.join(","),
+    AQE_V3_SWARM_SIZE: String(config.agents?.maxConcurrent ?? 15),
+    AQE_V3_TOPOLOGY: "hierarchical",
+    AQE_V3_SUBLINEAR_ENABLED: "true",
+    AQE_V3_HNSW_ENABLED: config.learning?.hnswConfig ? "true" : "false",
+    AQE_V3_HOOKS_ENABLED: "true",
+    AQE_V3_HOOK_BRIDGE: ".claude/hooks/v3-qe-bridge.sh",
+    AQE_V3_DOMAIN_WORKERS: ".claude/hooks/v3-domain-workers.json",
+    AQE_V3_AISP_ENABLED: "true",
+    AQE_V3_REASONING_BANK: ".agentic-qe/memory.db",
+    AQE_V3_PATTERN_PROMOTION_THRESHOLD: String(config.learning?.promotionThreshold ?? 3),
+    AQE_V3_SUCCESS_RATE_THRESHOLD: String(config.learning?.qualityThreshold ?? 0.7)
+  };
+}
+function generateV3SettingsSections(config) {
+  const domains = config.domains?.enabled || [];
+  return {
+    aqe: {
+      version: config.version ?? "3.0.0",
+      initialized: (/* @__PURE__ */ new Date()).toISOString(),
+      hooksConfigured: true
+    },
+    statusLine: {
+      type: "command",
+      command: 'node .claude/helpers/statusline-v3.cjs 2>/dev/null || .claude/statusline-v3.sh 2>/dev/null || echo "\u258A Agentic QE v3"',
+      refreshMs: 5e3,
+      enabled: true
+    },
+    permissions: {
+      allow: [
+        "Bash(npx claude-flow:*)",
+        "Bash(npx @claude-flow/cli:*)",
+        "mcp__claude-flow__:*",
+        "mcp__agentic_qe__*"
+      ],
+      deny: [
+        "Bash(rm -rf /)"
+      ]
+    },
+    includeCoAuthoredBy: true,
+    v3Configuration: {
+      domains: {
+        total: domains.length,
+        names: domains
+      },
+      swarm: {
+        totalAgents: config.agents?.maxConcurrent ?? 15,
+        topology: "hierarchical",
+        coordination: "queen-led"
+      }
+    },
+    v3Learning: {
+      enabled: config.learning?.enabled ?? true,
+      reasoningBank: {
+        dbPath: ".agentic-qe/memory.db",
+        enableHNSW: !!config.learning?.hnswConfig
+      },
+      patternPromotion: {
+        threshold: config.learning?.promotionThreshold ?? 3,
+        successRateMin: config.learning?.qualityThreshold ?? 0.7
+      }
+    }
+  };
+}
+
+// src/init/init-wizard-hooks.ts
 async function configureHooks(projectRoot, config) {
   if (!config.hooks.claudeCode) {
     return false;
@@ -116543,14 +116763,25 @@ async function configureHooks(projectRoot, config) {
       settings = {};
     }
   }
-  const hooks = {
+  const aqeHooks = {
     PreToolUse: [
       {
         matcher: "^(Write|Edit|MultiEdit)$",
         hooks: [
           {
             type: "command",
-            command: 'aqe hooks pre-edit --file "$TOOL_INPUT_file_path"',
+            command: 'npx agentic-qe hooks guard --file "$TOOL_INPUT_file_path" --json',
+            timeout: 3e3,
+            continueOnError: true
+          }
+        ]
+      },
+      {
+        matcher: "^(Write|Edit|MultiEdit)$",
+        hooks: [
+          {
+            type: "command",
+            command: 'npx agentic-qe hooks pre-edit --file "$TOOL_INPUT_file_path" --json',
             timeout: 5e3,
             continueOnError: true
           }
@@ -116561,8 +116792,8 @@ async function configureHooks(projectRoot, config) {
         hooks: [
           {
             type: "command",
-            command: 'aqe hooks pre-command --command "$TOOL_INPUT_command"',
-            timeout: 5e3,
+            command: 'npx agentic-qe hooks pre-command --command "$TOOL_INPUT_command" --json',
+            timeout: 3e3,
             continueOnError: true
           }
         ]
@@ -116572,7 +116803,7 @@ async function configureHooks(projectRoot, config) {
         hooks: [
           {
             type: "command",
-            command: 'aqe hooks pre-task --description "$TOOL_INPUT_prompt"',
+            command: 'npx agentic-qe hooks pre-task --description "$TOOL_INPUT_prompt" --json',
             timeout: 5e3,
             continueOnError: true
           }
@@ -116585,7 +116816,7 @@ async function configureHooks(projectRoot, config) {
         hooks: [
           {
             type: "command",
-            command: 'aqe hooks post-edit --file "$TOOL_INPUT_file_path" --success "$TOOL_SUCCESS"',
+            command: 'npx agentic-qe hooks post-edit --file "$TOOL_INPUT_file_path" --success --json',
             timeout: 5e3,
             continueOnError: true
           }
@@ -116596,7 +116827,7 @@ async function configureHooks(projectRoot, config) {
         hooks: [
           {
             type: "command",
-            command: 'aqe hooks post-command --command "$TOOL_INPUT_command" --success "$TOOL_SUCCESS"',
+            command: 'npx agentic-qe hooks post-command --command "$TOOL_INPUT_command" --success --json',
             timeout: 5e3,
             continueOnError: true
           }
@@ -116607,7 +116838,7 @@ async function configureHooks(projectRoot, config) {
         hooks: [
           {
             type: "command",
-            command: 'aqe hooks post-task --task-id "$TOOL_RESULT_agent_id" --success "$TOOL_SUCCESS"',
+            command: 'npx agentic-qe hooks post-task --task-id "$TOOL_RESULT_agent_id" --success --json',
             timeout: 5e3,
             continueOnError: true
           }
@@ -116619,7 +116850,7 @@ async function configureHooks(projectRoot, config) {
         hooks: [
           {
             type: "command",
-            command: 'aqe hooks route --task "$PROMPT"',
+            command: 'npx agentic-qe hooks route --task "$PROMPT" --json',
             timeout: 5e3,
             continueOnError: true
           }
@@ -116631,7 +116862,7 @@ async function configureHooks(projectRoot, config) {
         hooks: [
           {
             type: "command",
-            command: 'aqe hooks session-start --session-id "$SESSION_ID"',
+            command: 'npx agentic-qe hooks session-start --session-id "$SESSION_ID" --json',
             timeout: 1e4,
             continueOnError: true
           }
@@ -116643,7 +116874,7 @@ async function configureHooks(projectRoot, config) {
         hooks: [
           {
             type: "command",
-            command: "aqe hooks session-end --save-state",
+            command: "npx agentic-qe hooks session-end --save-state --json",
             timeout: 5e3,
             continueOnError: true
           }
@@ -116652,33 +116883,22 @@ async function configureHooks(projectRoot, config) {
     ]
   };
   const existingHooks = settings.hooks || {};
-  const mergedHooks = {};
-  for (const [hookType, hookArray] of Object.entries(hooks)) {
-    const existing = existingHooks[hookType] || [];
-    mergedHooks[hookType] = [...existing, ...hookArray];
-  }
-  for (const [hookType, hookArray] of Object.entries(existingHooks)) {
-    if (!mergedHooks[hookType]) {
-      mergedHooks[hookType] = hookArray;
-    }
-  }
-  settings.hooks = mergedHooks;
+  settings.hooks = mergeHooksSmart(existingHooks, aqeHooks);
   const existingEnv = settings.env || {};
   settings.env = {
     ...existingEnv,
-    AQE_MEMORY_PATH: ".agentic-qe/memory.db",
-    AQE_V3_MODE: "true",
-    AQE_LEARNING_ENABLED: config.learning.enabled ? "true" : "false"
+    ...generateAqeEnvVars(config)
   };
-  settings.aqe = {
-    version: config.version,
-    initialized: (/* @__PURE__ */ new Date()).toISOString(),
-    hooksConfigured: true
-  };
-  const existingMcp = settings.enabledMcpjsonServers || [];
-  if (!existingMcp.includes("aqe")) {
-    settings.enabledMcpjsonServers = [...existingMcp, "aqe"];
+  const v3Sections = generateV3SettingsSections(config);
+  for (const [key, value] of Object.entries(v3Sections)) {
+    settings[key] = value;
+  }
+  let existingMcp = settings.enabledMcpjsonServers || [];
+  existingMcp = existingMcp.filter((s70) => s70 !== "aqe");
+  if (!existingMcp.includes("agentic-qe")) {
+    existingMcp.push("agentic-qe");
   }
+  settings.enabledMcpjsonServers = existingMcp;
   writeFileSync3(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
   await installCrossPhaseMemoryHooks(projectRoot);
   return true;
@@ -118290,6 +118510,7 @@ function createN8nInstaller(options) {
 
 // src/init/init-wizard-steps.ts
 init_error_utils();
+init_safe_db();
 async function initializePersistenceDatabase(projectRoot) {
   let Database = null;
   try {
@@ -118349,8 +118570,7 @@ 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'
@@ -118403,8 +118623,7 @@ 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%'
@@ -119079,10 +119298,9 @@ 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";
@@ -119171,8 +119389,7 @@ 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
@@ -119442,6 +119659,7 @@ 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 = [
@@ -119511,8 +119729,7 @@ 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'
@@ -119529,8 +119746,7 @@ 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%'
@@ -119609,8 +119825,7 @@ 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'
@@ -119677,13 +119892,18 @@ var HooksPhase = class extends BasePhase {
       return {
         configured: false,
         settingsPath: "",
-        hookTypes: []
+        hookTypes: [],
+        existingAqeDetected: false
       };
     }
     const claudeDir = join27(projectRoot, ".claude");
     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)) {
@@ -119694,61 +119914,131 @@ var HooksPhase = class extends BasePhase {
         settings = {};
       }
     }
-    const hooks = this.generateHooksConfig(config);
-    const hookTypes = Object.keys(hooks);
+    const aqeHooks = this.generateHooksConfig(config);
+    const hookTypes = Object.keys(aqeHooks);
     const existingHooks = settings.hooks || {};
-    const mergedHooks = {};
-    for (const [hookType, hookArray] of Object.entries(hooks)) {
-      const existing = existingHooks[hookType] || [];
-      const newHooks = hookArray;
-      const existingCommands = /* @__PURE__ */ new Set();
-      for (const hook of existing) {
-        const h66 = hook;
-        if (h66.hooks) {
-          for (const innerHook of h66.hooks) {
-            if (innerHook.command) {
-              existingCommands.add(innerHook.command);
-            }
-          }
-        }
-      }
-      const uniqueNewHooks = newHooks.filter((hook) => {
-        if (!hook.hooks) return true;
-        return !hook.hooks.some((h66) => h66.command && existingCommands.has(h66.command));
-      });
-      mergedHooks[hookType] = [...existing, ...uniqueNewHooks];
+    const existingAqeDetected = this.hasExistingAqeHooks(existingHooks);
+    if (existingAqeDetected) {
+      context2.services.log("  Detected existing AQE hooks \u2014 replacing with updated config");
     }
-    for (const [hookType, hookArray] of Object.entries(existingHooks)) {
-      if (!mergedHooks[hookType]) {
-        mergedHooks[hookType] = hookArray;
-      }
-    }
-    settings.hooks = mergedHooks;
+    settings.hooks = mergeHooksSmart(existingHooks, aqeHooks);
     const existingEnv = settings.env || {};
     settings.env = {
       ...existingEnv,
-      AQE_MEMORY_PATH: ".agentic-qe/memory.db",
-      AQE_V3_MODE: "true",
-      AQE_LEARNING_ENABLED: config.learning.enabled ? "true" : "false"
+      ...generateAqeEnvVars(config)
     };
-    settings.aqe = {
-      version: config.version,
-      initialized: (/* @__PURE__ */ new Date()).toISOString(),
-      hooksConfigured: true
-    };
-    const existingMcp = settings.enabledMcpjsonServers || [];
-    if (!existingMcp.includes("aqe")) {
-      settings.enabledMcpjsonServers = [...existingMcp, "aqe"];
+    const v3Sections = generateV3SettingsSections(config);
+    for (const [key, value] of Object.entries(v3Sections)) {
+      settings[key] = value;
+    }
+    let existingMcp = settings.enabledMcpjsonServers || [];
+    existingMcp = existingMcp.filter((s70) => s70 !== "aqe");
+    if (!existingMcp.includes("agentic-qe")) {
+      existingMcp.push("agentic-qe");
     }
+    settings.enabledMcpjsonServers = existingMcp;
     writeFileSync9(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
+    this.writeHooksReadme(hooksDir, hookTypes);
+    this.installHookAssets(hooksDir, context2);
     context2.services.log(`  Settings: ${settingsPath}`);
+    context2.services.log(`  Hooks dir: ${hooksDir}`);
     context2.services.log(`  Hook types: ${hookTypes.join(", ")}`);
     return {
       configured: true,
       settingsPath,
-      hookTypes
+      hookTypes,
+      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
+   */
+  hasExistingAqeHooks(hooks) {
+    for (const hookArray of Object.values(hooks)) {
+      if (!Array.isArray(hookArray)) continue;
+      for (const entry of hookArray) {
+        if (isAqeHookEntry(entry)) return true;
+      }
+    }
+    return false;
+  }
   /**
    * Generate hooks configuration
    *
@@ -120592,8 +120882,7 @@ 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";
@@ -120650,8 +120939,7 @@ 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 (
@@ -123090,6 +123378,116 @@ function createCommandRegistry(context2, cleanupAndExit2, ensureInitialized2) {
 // src/cli/commands/test.ts
 import { Command } from "commander";
 import chalk9 from "chalk";
+
+// src/cli/utils/file-discovery.ts
+import { existsSync as existsSync35, readdirSync as readdirSync10, statSync as statSync9 } from "fs";
+import { join as join37, extname as extname7 } from "path";
+var SOURCE_EXTENSIONS = /* @__PURE__ */ new Set([
+  // JavaScript / TypeScript
+  ".ts",
+  ".tsx",
+  ".js",
+  ".jsx",
+  ".mjs",
+  ".cjs",
+  // Python
+  ".py",
+  ".pyw",
+  // Go
+  ".go",
+  // Rust
+  ".rs",
+  // Java / Kotlin
+  ".java",
+  ".kt",
+  ".kts",
+  // Ruby
+  ".rb",
+  // C#
+  ".cs",
+  // PHP
+  ".php",
+  // Swift
+  ".swift",
+  // C / C++
+  ".c",
+  ".h",
+  ".cpp",
+  ".hpp",
+  ".cc",
+  // Scala
+  ".scala"
+]);
+var TEST_PATTERNS = [".test.", ".spec.", "_test.", "_spec."];
+var SKIP_DIRS = /* @__PURE__ */ new Set([
+  "node_modules",
+  "dist",
+  "build",
+  "coverage",
+  ".git",
+  "__pycache__",
+  ".venv",
+  "venv",
+  ".tox",
+  ".mypy_cache",
+  "target",
+  ".gradle",
+  "vendor",
+  ".bundle",
+  ".next",
+  ".nuxt",
+  ".output"
+]);
+function walkSourceFiles(targetPath, options = {}) {
+  const {
+    maxDepth = 6,
+    includeTests = false,
+    testsOnly = false,
+    extraExtensions = []
+  } = options;
+  if (!existsSync35(targetPath)) {
+    return [];
+  }
+  const stat4 = statSync9(targetPath);
+  if (stat4.isFile()) {
+    return [targetPath];
+  }
+  if (!stat4.isDirectory()) {
+    return [];
+  }
+  const extraSet = new Set(extraExtensions.map((e20) => e20.startsWith(".") ? e20 : `.${e20}`));
+  const result = [];
+  function walk(dir, depth) {
+    if (depth > maxDepth) return;
+    let entries;
+    try {
+      entries = readdirSync10(dir, { withFileTypes: true });
+    } catch {
+      return;
+    }
+    for (const entry of entries) {
+      if (entry.isDirectory()) {
+        if (SKIP_DIRS.has(entry.name)) continue;
+        walk(join37(dir, entry.name), depth + 1);
+      } else if (entry.isFile()) {
+        const ext = extname7(entry.name).toLowerCase();
+        const isSourceExt = SOURCE_EXTENSIONS.has(ext) || extraSet.has(ext);
+        if (!isSourceExt) continue;
+        if (entry.name.endsWith(".d.ts")) continue;
+        const isTestFile2 = TEST_PATTERNS.some((p74) => entry.name.includes(p74)) || entry.name.startsWith("test_");
+        if (testsOnly) {
+          if (isTestFile2) result.push(join37(dir, entry.name));
+        } else if (includeTests || !isTestFile2) {
+          result.push(join37(dir, entry.name));
+        }
+      }
+    }
+  }
+  walk(targetPath, 0);
+  return result;
+}
+
+// src/cli/commands/test.ts
 function createTestCommand(context2, cleanupAndExit2, ensureInitialized2) {
   const testCmd = new Command("test").description("Test generation shortcut").argument("<action>", "Action (generate|execute)").argument("[target]", "Target file or directory").option("-f, --framework <framework>", "Test framework", "vitest").option("-t, --type <type>", "Test type (unit|integration|e2e)", "unit").action(async (action, target, options) => {
     if (!await ensureInitialized2()) return;
@@ -123103,33 +123501,9 @@ function createTestCommand(context2, cleanupAndExit2, ensureInitialized2) {
           console.log(chalk9.red("Test generation domain not available"));
           return;
         }
-        const fs23 = await import("fs");
         const path26 = await import("path");
         const targetPath = path26.resolve(target || ".");
-        let sourceFiles = [];
-        if (fs23.existsSync(targetPath)) {
-          if (fs23.statSync(targetPath).isDirectory()) {
-            const walkDir2 = (dir, depth = 0) => {
-              if (depth > 4) return [];
-              const result2 = [];
-              const items = fs23.readdirSync(dir);
-              for (const item of items) {
-                if (item === "node_modules" || item === "dist" || item === "tests" || item.includes(".test.") || item.includes(".spec.")) continue;
-                const fullPath = path26.join(dir, item);
-                const stat4 = fs23.statSync(fullPath);
-                if (stat4.isDirectory()) {
-                  result2.push(...walkDir2(fullPath, depth + 1));
-                } else if (item.endsWith(".ts") && !item.endsWith(".d.ts")) {
-                  result2.push(fullPath);
-                }
-              }
-              return result2;
-            };
-            sourceFiles = walkDir2(targetPath);
-          } else {
-            sourceFiles = [targetPath];
-          }
-        }
+        const sourceFiles = walkSourceFiles(targetPath, { includeTests: false });
         if (sourceFiles.length === 0) {
           console.log(chalk9.yellow("No source files found"));
           return;
@@ -123180,33 +123554,9 @@ function createTestCommand(context2, cleanupAndExit2, ensureInitialized2) {
           console.log(chalk9.red("Test execution domain not available"));
           return;
         }
-        const fs23 = await import("fs");
         const path26 = await import("path");
         const targetPath = path26.resolve(target || ".");
-        let testFiles = [];
-        if (fs23.existsSync(targetPath)) {
-          if (fs23.statSync(targetPath).isDirectory()) {
-            const walkDir2 = (dir, depth = 0) => {
-              if (depth > 4) return [];
-              const result2 = [];
-              const items = fs23.readdirSync(dir);
-              for (const item of items) {
-                if (item === "node_modules" || item === "dist") continue;
-                const fullPath = path26.join(dir, item);
-                const stat4 = fs23.statSync(fullPath);
-                if (stat4.isDirectory()) {
-                  result2.push(...walkDir2(fullPath, depth + 1));
-                } else if ((item.includes(".test.") || item.includes(".spec.")) && item.endsWith(".ts")) {
-                  result2.push(fullPath);
-                }
-              }
-              return result2;
-            };
-            testFiles = walkDir2(targetPath);
-          } else {
-            testFiles = [targetPath];
-          }
-        }
+        const testFiles = walkSourceFiles(targetPath, { testsOnly: true });
         if (testFiles.length === 0) {
           console.log(chalk9.yellow("No test files found"));
           return;
@@ -123283,13 +123633,13 @@ var BaseWizardCommand = class {
 
 // src/cli/wizards/core/wizard-step.ts
 import chalk11 from "chalk";
-import { existsSync as existsSync36 } from "fs";
+import { existsSync as existsSync37 } from "fs";
 import { resolve as resolve8 } from "path";
 
 // src/cli/wizards/core/wizard-utils.ts
 import chalk10 from "chalk";
-import { existsSync as existsSync35, statSync as statSync9 } from "fs";
-import { join as join37, relative as relative6 } from "path";
+import { existsSync as existsSync36, statSync as statSync10 } from "fs";
+import { join as join38, relative as relative6 } from "path";
 var WizardPrompt = class {
   /**
    * Generic prompt helper - wraps readline.question in a Promise
@@ -123380,8 +123730,8 @@ var WizardSuggestions = class _WizardSuggestions {
     const suggestions = [];
     const commonDirs = ["src", "lib", "app", "packages", "api"];
     for (const dir of commonDirs) {
-      const dirPath = join37(cwd, dir);
-      if (existsSync35(dirPath) && statSync9(dirPath).isDirectory()) {
+      const dirPath = join38(cwd, dir);
+      if (existsSync36(dirPath) && statSync10(dirPath).isDirectory()) {
         suggestions.push(dir);
       }
     }
@@ -123399,8 +123749,8 @@ var WizardSuggestions = class _WizardSuggestions {
       ".nyc_output"
     ];
     for (const loc of coverageLocations) {
-      const locPath = join37(cwd, loc);
-      if (existsSync35(locPath)) {
+      const locPath = join38(cwd, loc);
+      if (existsSync36(locPath)) {
         suggestions.push(loc);
       }
     }
@@ -123422,8 +123772,8 @@ var WizardSuggestions = class _WizardSuggestions {
       "Dockerfile"
     ];
     for (const file of securityFiles) {
-      const filePath = join37(cwd, file);
-      if (existsSync35(filePath)) {
+      const filePath = join38(cwd, file);
+      if (existsSync36(filePath)) {
         suggestions.push(file);
       }
     }
@@ -123436,13 +123786,13 @@ var WizardSuggestions = class _WizardSuggestions {
     const suggestions = [];
     const commonDirs = ["src", "lib", "app", "packages"];
     for (const dir of commonDirs) {
-      const dirPath = join37(cwd, dir);
-      if (existsSync35(dirPath) && statSync9(dirPath).isDirectory()) {
+      const dirPath = join38(cwd, dir);
+      if (existsSync36(dirPath) && statSync10(dirPath).isDirectory()) {
         suggestions.push(`${dir}/**/*.ts`);
         suggestions.push(dir);
       }
     }
-    if (existsSync35(join37(cwd, "src"))) {
+    if (existsSync36(join38(cwd, "src"))) {
       suggestions.push("src/services/**/*.ts");
       suggestions.push("src/utils/**/*.ts");
       suggestions.push("src/components/**/*.tsx");
@@ -123454,12 +123804,12 @@ var WizardSuggestions = class _WizardSuggestions {
    */
   static checkPatternsExist(cwd) {
     const patternLocations = [
-      join37(cwd, ".agentic-qe", "patterns"),
-      join37(cwd, ".agentic-qe", "memory.db"),
-      join37(cwd, ".aqe", "patterns"),
-      join37(cwd, "data", "patterns")
+      join38(cwd, ".agentic-qe", "patterns"),
+      join38(cwd, ".agentic-qe", "memory.db"),
+      join38(cwd, ".aqe", "patterns"),
+      join38(cwd, "data", "patterns")
     ];
-    return patternLocations.some((loc) => existsSync35(loc));
+    return patternLocations.some((loc) => existsSync36(loc));
   }
 };
 var WizardFormat = class {
@@ -123736,7 +124086,7 @@ var PathInputStep = class extends BaseWizardCommand {
   async execute(context2) {
     if (context2.nonInteractive) {
       const resolved2 = resolve8(context2.cwd, this.defaultValue);
-      return this.success(existsSync36(resolved2) ? resolved2 : context2.cwd);
+      return this.success(existsSync37(resolved2) ? resolved2 : context2.cwd);
     }
     WizardPrompt.printStepHeader(this.stepNumber, this.title, this.description);
     if (this.examples) {
@@ -123759,7 +124109,7 @@ var PathInputStep = class extends BaseWizardCommand {
     );
     const value = input.trim() || this.defaultValue;
     const resolved = resolve8(context2.cwd, value);
-    if (this.validatePath && !existsSync36(resolved)) {
+    if (this.validatePath && !existsSync37(resolved)) {
       console.log(chalk11.yellow(`  Warning: '${value}' does not exist, using current directory.`));
       return this.success(context2.cwd);
     }
@@ -124111,30 +124461,7 @@ function createCoverageCommand(context2, cleanupAndExit2, ensureInitialized2) {
       const fs23 = await import("fs");
       const path26 = await import("path");
       const targetPath = path26.resolve(analyzeTarget);
-      let sourceFiles = [];
-      if (fs23.existsSync(targetPath)) {
-        if (fs23.statSync(targetPath).isDirectory()) {
-          const walkDir2 = (dir, depth = 0) => {
-            if (depth > 4) return [];
-            const result2 = [];
-            const items = fs23.readdirSync(dir);
-            for (const item of items) {
-              if (item === "node_modules" || item === "dist") continue;
-              const fullPath = path26.join(dir, item);
-              const stat4 = fs23.statSync(fullPath);
-              if (stat4.isDirectory()) {
-                result2.push(...walkDir2(fullPath, depth + 1));
-              } else if (item.endsWith(".ts") && !item.endsWith(".d.ts")) {
-                result2.push(fullPath);
-              }
-            }
-            return result2;
-          };
-          sourceFiles = walkDir2(targetPath);
-        } else {
-          sourceFiles = [targetPath];
-        }
-      }
+      const sourceFiles = walkSourceFiles(targetPath, { includeTests: false });
       if (sourceFiles.length === 0) {
         console.log(chalk13.yellow("No source files found"));
         return;
@@ -124320,33 +124647,9 @@ function createSecurityCommand(context2, cleanupAndExit2, ensureInitialized2) {
         console.log(chalk15.red("Security domain not available"));
         return;
       }
-      const fs23 = await import("fs");
       const path26 = await import("path");
       const targetPath = path26.resolve(options.target);
-      let files = [];
-      if (fs23.existsSync(targetPath)) {
-        if (fs23.statSync(targetPath).isDirectory()) {
-          const walkDir2 = (dir, depth = 0) => {
-            if (depth > 4) return [];
-            const result = [];
-            const items = fs23.readdirSync(dir);
-            for (const item of items) {
-              if (item === "node_modules" || item === "dist") continue;
-              const fullPath = path26.join(dir, item);
-              const stat4 = fs23.statSync(fullPath);
-              if (stat4.isDirectory()) {
-                result.push(...walkDir2(fullPath, depth + 1));
-              } else if (item.endsWith(".ts") && !item.endsWith(".d.ts")) {
-                result.push(fullPath);
-              }
-            }
-            return result;
-          };
-          files = walkDir2(targetPath);
-        } else {
-          files = [targetPath];
-        }
-      }
+      const files = walkSourceFiles(targetPath, { includeTests: true });
       if (files.length === 0) {
         console.log(chalk15.yellow("No files found to scan"));
         return;
@@ -124421,37 +124724,15 @@ function createCodeCommand(context2, cleanupAndExit2, ensureInitialized2) {
         console.log(chalk16.red("Code intelligence domain not available"));
         return;
       }
-      const fs23 = await import("fs");
       const path26 = await import("path");
       if (action === "index") {
         console.log(chalk16.blue(`
  Indexing codebase at ${target || "."}...
 `));
         const targetPath = path26.resolve(target || ".");
-        let paths = [];
-        if (fs23.existsSync(targetPath)) {
-          if (fs23.statSync(targetPath).isDirectory()) {
-            const walkDir2 = (dir, depth = 0) => {
-              if (depth > 4) return [];
-              const result2 = [];
-              const items = fs23.readdirSync(dir);
-              for (const item of items) {
-                if (item === "node_modules" || item === "dist") continue;
-                const fullPath = path26.join(dir, item);
-                const stat4 = fs23.statSync(fullPath);
-                if (stat4.isDirectory()) {
-                  result2.push(...walkDir2(fullPath, depth + 1));
-                } else if (item.endsWith(".ts") && !item.endsWith(".d.ts")) {
-                  result2.push(fullPath);
-                }
-              }
-              return result2;
-            };
-            paths = walkDir2(targetPath);
-          } else {
-            paths = [targetPath];
-          }
-        }
+        const paths = walkSourceFiles(targetPath, {
+          includeTests: options.includeTests || false
+        });
         console.log(chalk16.gray(`  Found ${paths.length} files to index...
 `));
         const result = await codeAPI.index({
@@ -124510,30 +124791,7 @@ function createCodeCommand(context2, cleanupAndExit2, ensureInitialized2) {
  Analyzing impact for ${target || "recent changes"}...
 `));
         const targetPath = path26.resolve(target || ".");
-        let changedFiles = [];
-        if (fs23.existsSync(targetPath)) {
-          if (fs23.statSync(targetPath).isFile()) {
-            changedFiles = [targetPath];
-          } else {
-            const walkDir2 = (dir, depth = 0) => {
-              if (depth > 2) return [];
-              const result2 = [];
-              const items = fs23.readdirSync(dir);
-              for (const item of items) {
-                if (item === "node_modules" || item === "dist") continue;
-                const fullPath = path26.join(dir, item);
-                const stat4 = fs23.statSync(fullPath);
-                if (stat4.isDirectory()) {
-                  result2.push(...walkDir2(fullPath, depth + 1));
-                } else if (item.endsWith(".ts") && !item.endsWith(".d.ts")) {
-                  result2.push(fullPath);
-                }
-              }
-              return result2;
-            };
-            changedFiles = walkDir2(targetPath).slice(0, 10);
-          }
-        }
+        const changedFiles = walkSourceFiles(targetPath, { maxDepth: 2 }).slice(0, 10);
         const result = await codeAPI.analyzeImpact({
           changedFiles,
           depth: parseInt(options.depth),
@@ -124579,30 +124837,7 @@ function createCodeCommand(context2, cleanupAndExit2, ensureInitialized2) {
  Mapping dependencies for ${target || "."}...
 `));
         const targetPath = path26.resolve(target || ".");
-        let files = [];
-        if (fs23.existsSync(targetPath)) {
-          if (fs23.statSync(targetPath).isFile()) {
-            files = [targetPath];
-          } else {
-            const walkDir2 = (dir, depth = 0) => {
-              if (depth > 2) return [];
-              const result2 = [];
-              const items = fs23.readdirSync(dir);
-              for (const item of items) {
-                if (item === "node_modules" || item === "dist") continue;
-                const fullPath = path26.join(dir, item);
-                const stat4 = fs23.statSync(fullPath);
-                if (stat4.isDirectory()) {
-                  result2.push(...walkDir2(fullPath, depth + 1));
-                } else if (item.endsWith(".ts") && !item.endsWith(".d.ts")) {
-                  result2.push(fullPath);
-                }
-              }
-              return result2;
-            };
-            files = walkDir2(targetPath).slice(0, 50);
-          }
-        }
+        const files = walkSourceFiles(targetPath, { maxDepth: 2 }).slice(0, 50);
         const result = await codeAPI.mapDependencies({
           files,
           direction: "both",
@@ -124877,7 +125112,7 @@ function createMigrateCommand(context2, cleanupAndExit2, ensureInitialized2) {
           migratedFrom: "v2",
           migratedAt: (/* @__PURE__ */ new Date()).toISOString(),
           hnswEnabled: true,
-          vectorDimensions: 128
+          vectorDimensions: 768
         }, null, 2));
         const stats = fs23.statSync(v2Files.memoryDb);
         console.log(chalk17.green(`   * Memory database migrated (${(stats.size / 1024).toFixed(1)} KB)
@@ -124906,7 +125141,7 @@ 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 },
@@ -126847,9 +127082,10 @@ import chalk20 from "chalk";
 
 // src/init/fleet-integration.ts
 init_error_utils();
+init_safe_db();
 import chalk19 from "chalk";
-import { existsSync as existsSync37 } from "fs";
-import { join as join39 } from "path";
+import { existsSync as existsSync38 } from "fs";
+import { join as join40 } from "path";
 var FleetInitEnhancer = class {
   projectRoot;
   options;
@@ -126961,7 +127197,7 @@ var FleetInitEnhancer = class {
       });
       console.log(chalk19.gray(`  Indexing ${files.length} files...`));
       const result = await kgService.index({
-        paths: files.map((f74) => join39(this.projectRoot, f74)),
+        paths: files.map((f74) => join40(this.projectRoot, f74)),
         incremental: false,
         includeTests: true
       });
@@ -126996,13 +127232,12 @@ var FleetInitEnhancer = class {
    * Checks the memory database for code-intelligence:kg namespace entries
    */
   async hasCodeIntelligenceIndex() {
-    const dbPath = join39(this.projectRoot, ".agentic-qe", "memory.db");
-    if (!existsSync37(dbPath)) {
+    const dbPath = join40(this.projectRoot, ".agentic-qe", "memory.db");
+    if (!existsSync38(dbPath)) {
       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'
@@ -127017,10 +127252,9 @@ var FleetInitEnhancer = class {
    * Get count of knowledge graph entries
    */
   async getKGEntryCount() {
-    const dbPath = join39(this.projectRoot, ".agentic-qe", "memory.db");
+    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%'
@@ -128523,7 +128757,7 @@ function createParallelEvalRunner(skillValidationLearner, config = {}, executor2
 
 // src/validation/validation-result-aggregator.ts
 init_safe_json();
-import { readFileSync as readFileSync28, writeFileSync as writeFileSync17, existsSync as existsSync39 } from "fs";
+import { readFileSync as readFileSync28, writeFileSync as writeFileSync17, existsSync as existsSync40 } from "fs";
 var DEFAULT_CONFIG60 = {
   varianceThreshold: 0.04,
   // ~20% standard deviation
@@ -128868,7 +129102,7 @@ var ValidationResultAggregator = class {
    * Update trust tier manifest with new pass rates
    */
   async updateManifest(report) {
-    if (!existsSync39(this.manifestPath)) {
+    if (!existsSync40(this.manifestPath)) {
       throw new Error(`Manifest file not found: ${this.manifestPath}`);
     }
     const manifest = safeJsonParse(readFileSync28(this.manifestPath, "utf-8"));
@@ -130655,18 +130889,18 @@ function formatDuration2(ms) {
 // src/cli/commands/validate.ts
 init_safe_json();
 import { Command as Command10 } from "commander";
-import { readFileSync as readFileSync29, writeFileSync as writeFileSync18, existsSync as existsSync40, readdirSync as readdirSync10, statSync as statSync11 } from "fs";
-import { join as join41, resolve as resolve9, basename as basename7 } from "path";
+import { readFileSync as readFileSync29, writeFileSync as writeFileSync18, existsSync as existsSync41, readdirSync as readdirSync11, statSync as statSync12 } from "fs";
+import { join as join42, resolve as resolve9, basename as basename7 } from "path";
 import chalk22 from "chalk";
 function loadValidationResults(inputPath) {
   const resolvedPath = resolve9(inputPath);
-  if (!existsSync40(resolvedPath)) {
+  if (!existsSync41(resolvedPath)) {
     throw new Error(`Input path not found: ${resolvedPath}`);
   }
-  const stat4 = statSync11(resolvedPath);
+  const stat4 = statSync12(resolvedPath);
   if (stat4.isDirectory()) {
     const results = [];
-    const files = readdirSync10(resolvedPath).filter((f74) => f74.endsWith(".json")).map((f74) => join41(resolvedPath, f74));
+    const files = readdirSync11(resolvedPath).filter((f74) => f74.endsWith(".json")).map((f74) => join42(resolvedPath, f74));
     for (const file of files) {
       try {
         const content = safeJsonParse(readFileSync29(file, "utf-8"));
@@ -130716,15 +130950,15 @@ function createMockLearner() {
 function getDefaultManifestPath() {
   const cwd = process.cwd();
   const candidates = [
-    join41(cwd, ".claude/skills/trust-tier-manifest.json"),
-    join41(cwd, ".claude/skills/skills-manifest.json")
+    join42(cwd, ".claude/skills/trust-tier-manifest.json"),
+    join42(cwd, ".claude/skills/skills-manifest.json")
   ];
   for (const candidate of candidates) {
-    if (existsSync40(candidate)) {
+    if (existsSync41(candidate)) {
       return candidate;
     }
   }
-  return join41(cwd, ".claude/skills/trust-tier-manifest.json");
+  return join42(cwd, ".claude/skills/trust-tier-manifest.json");
 }
 function writeReport(report, aggregator, options) {
   const format = options.format || "markdown";
@@ -132455,7 +132689,7 @@ 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();
@@ -132483,7 +132717,7 @@ 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}`);
@@ -133849,7 +134083,7 @@ async function syncIncrementalToCloud(since, config) {
 }
 
 // src/integrations/embeddings/cache/EmbeddingCache.ts
-init_better_sqlite3();
+init_safe_db();
 init_unified_memory();
 init_safe_json();
 
@@ -133858,7 +134092,7 @@ 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();
@@ -136813,10 +137047,10 @@ 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 join43 } from "node:path";
-import { readFileSync as readFileSync32, existsSync as existsSync43 } from "node:fs";
+import { dirname as dirname13, join as join44 } from "node:path";
+import { readFileSync as readFileSync32, existsSync as existsSync44 } from "node:fs";
 var FALLBACK_RETRY_DELAYS_MS = [1e3, 2e3, 4e3];
 var WasmLoader = class {
   state = "unloaded";
@@ -137069,20 +137303,20 @@ 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");
-            return join43(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
+            const modulePath = require2.resolve("prime-radiant-advanced-wasm");
+            return join44(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
           } catch {
             return null;
           }
         })(),
-        join43(process.cwd(), "node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm")
+        join44(process.cwd(), "node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm")
       ].filter((p74) => p74 !== null);
       for (const path26 of wasmPaths) {
-        if (existsSync43(path26)) {
+        if (existsSync44(path26)) {
           return true;
         }
       }
@@ -137275,18 +137509,18 @@ 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)}`
@@ -137295,7 +137529,7 @@ 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();
@@ -137327,25 +137561,25 @@ 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");
-          return join43(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
+          const modulePath = require2.resolve("prime-radiant-advanced-wasm");
+          return join44(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
         } catch {
           return null;
         }
       })(),
       // Direct node_modules path from current file
-      join43(dirname13(fileURLToPath6(import.meta.url)), "../../../../node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm"),
+      join44(dirname13(fileURLToPath6(import.meta.url)), "../../../../node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm"),
       // Workspace root
-      join43(process.cwd(), "node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm")
+      join44(process.cwd(), "node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm")
     ].filter((p74) => p74 !== null);
     let wasmPath = null;
     for (const path26 of wasmPaths) {
-      if (existsSync43(path26)) {
+      if (existsSync44(path26)) {
         wasmPath = path26;
         break;
       }
@@ -138555,16 +138789,16 @@ init_qe_patterns();
 import { Command as Command16 } from "commander";
 import chalk29 from "chalk";
 import path25 from "node:path";
-import { existsSync as existsSync45, writeFileSync as writeFileSync22, readFileSync as readFileSync33, mkdirSync as mkdirSync19, copyFileSync as copyFileSync8 } from "node:fs";
+import { existsSync as existsSync46, writeFileSync as writeFileSync22, readFileSync as readFileSync33, mkdirSync as mkdirSync19, copyFileSync as copyFileSync8 } from "node:fs";
 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();
 import path23 from "node:path";
-import { existsSync as existsSync44 } from "node:fs";
+import { existsSync as existsSync45 } from "node:fs";
 var logger18 = LoggerFactory.create("metrics-tracker");
 var LearningMetricsTracker = class {
   db = null;
@@ -138578,10 +138812,10 @@ var LearningMetricsTracker = class {
    */
   async initialize() {
     if (this.initialized) return;
-    if (!existsSync44(this.dbPath)) {
+    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;
   }
@@ -138929,9 +139163,13 @@ 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";
@@ -139080,8 +139318,7 @@ 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") {
@@ -139098,8 +139335,7 @@ 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();
@@ -139367,7 +139603,7 @@ function registerImportCommand(learning) {
   learning.command("import").description("Import patterns from file").requiredOption("-i, --input <file>", "Input file path").option("--dry-run", "Show what would be imported without making changes").option("--json", "Output as JSON").action(async (options) => {
     try {
       const inputPath = path25.resolve(options.input);
-      if (!existsSync45(inputPath)) throw new Error(`File not found: ${inputPath}`);
+      if (!existsSync46(inputPath)) throw new Error(`File not found: ${inputPath}`);
       const content = readFileSync33(inputPath, "utf-8");
       const importData = safeJsonParse(content);
       if (!importData.patterns || !Array.isArray(importData.patterns)) throw new Error("Invalid pattern file format");
@@ -139436,7 +139672,7 @@ function registerResetCommand(learning) {
       if (!options.patternsOnly) filesToReset.push(path25.join(dataDir, "data", "learning-config.json"));
       console.log(chalk29.bold("\n\u{1F5D1}\uFE0F  Resetting Learning Data\n"));
       for (const file of filesToReset) {
-        if (existsSync45(file)) console.log(chalk29.dim(`  Removing: ${path25.relative(projectRoot, file)}`));
+        if (existsSync46(file)) console.log(chalk29.dim(`  Removing: ${path25.relative(projectRoot, file)}`));
       }
       printSuccess2('Learning data reset. Run "aqe init --auto" to reinitialize.\n');
       process.exit(0);
@@ -139451,15 +139687,14 @@ function registerExtractCommand(learning) {
     try {
       const projectRoot = findProjectRoot();
       const dbPath = path25.join(projectRoot, ".agentic-qe", "memory.db");
-      if (!existsSync45(dbPath)) throw new Error('No memory database found. Run "aqe init --auto" first.');
+      if (!existsSync46(dbPath)) throw new Error('No memory database found. Run "aqe init --auto" first.');
       const minReward = parseFloat(options.minReward);
       const minCount = parseInt(options.minCount, 10);
       console.log(chalk29.bold("\n\u{1F52C} Pattern Extraction from Learning Experiences\n"));
       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
@@ -139605,22 +139840,22 @@ function registerBackupCommand(learning) {
   learning.command("backup").description("Backup learning database to a file").option("-o, --output <path>", "Output file path").option("--compress", "Compress backup with gzip").option("--verify", "Verify backup integrity after creation").option("--json", "Output as JSON").action(async (options) => {
     try {
       const dbPath = getDbPath();
-      if (!existsSync45(dbPath)) throw new Error(`No learning database found at: ${dbPath}`);
+      if (!existsSync46(dbPath)) throw new Error(`No learning database found at: ${dbPath}`);
       const timestamp = (/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, 19);
       const defaultOutput = path25.join(process.cwd(), "backups", `learning-${timestamp}.db`);
       let outputPath = options.output ? path25.resolve(options.output) : defaultOutput;
       const backupDir = path25.dirname(outputPath);
-      if (!existsSync45(backupDir)) mkdirSync19(backupDir, { recursive: true });
+      if (!existsSync46(backupDir)) mkdirSync19(backupDir, { recursive: true });
       const sourceStats = await stat3(dbPath);
       const sourceSizeKB = (sourceStats.size / 1024).toFixed(2);
       copyFileSync8(dbPath, outputPath);
       const walPath = `${dbPath}-wal`;
-      if (existsSync45(walPath)) copyFileSync8(walPath, `${outputPath}-wal`);
+      if (existsSync46(walPath)) copyFileSync8(walPath, `${outputPath}-wal`);
       let finalPath = outputPath;
       if (options.compress) {
         finalPath = await compressFile(outputPath);
         await unlink(outputPath);
-        if (existsSync45(`${outputPath}-wal`)) await unlink(`${outputPath}-wal`);
+        if (existsSync46(`${outputPath}-wal`)) await unlink(`${outputPath}-wal`);
       }
       const finalStats = await stat3(finalPath);
       const finalSizeKB = (finalStats.size / 1024).toFixed(2);
@@ -139658,7 +139893,7 @@ function registerRestoreCommand(learning) {
     try {
       const inputPath = path25.resolve(options.input);
       const dbPath = getDbPath();
-      if (!existsSync45(inputPath)) throw new Error(`Backup file not found: ${inputPath}`);
+      if (!existsSync46(inputPath)) throw new Error(`Backup file not found: ${inputPath}`);
       const isCompressed = inputPath.endsWith(".gz");
       let restorePath = inputPath;
       if (isCompressed) {
@@ -139669,23 +139904,23 @@ function registerRestoreCommand(learning) {
       if (options.verify) {
         const verificationResult = await verifyDatabaseIntegrity(restorePath);
         if (!verificationResult.valid) {
-          if (isCompressed && existsSync45(restorePath)) await unlink(restorePath);
+          if (isCompressed && existsSync46(restorePath)) await unlink(restorePath);
           throw new Error(`Backup verification failed: ${verificationResult.message}`);
         }
       }
-      if (existsSync45(dbPath) && !options.force) {
+      if (existsSync46(dbPath) && !options.force) {
         printError2(`Database already exists at: ${dbPath}`);
         console.log(chalk29.yellow("  Use --force to overwrite"));
-        if (isCompressed && existsSync45(restorePath)) await unlink(restorePath);
+        if (isCompressed && existsSync46(restorePath)) await unlink(restorePath);
         process.exit(1);
       }
       const targetDir = path25.dirname(dbPath);
-      if (!existsSync45(targetDir)) mkdirSync19(targetDir, { recursive: true });
-      if (existsSync45(dbPath)) await unlink(dbPath);
-      if (existsSync45(`${dbPath}-wal`)) await unlink(`${dbPath}-wal`);
-      if (existsSync45(`${dbPath}-shm`)) await unlink(`${dbPath}-shm`);
+      if (!existsSync46(targetDir)) mkdirSync19(targetDir, { recursive: true });
+      if (existsSync46(dbPath)) await unlink(dbPath);
+      if (existsSync46(`${dbPath}-wal`)) await unlink(`${dbPath}-wal`);
+      if (existsSync46(`${dbPath}-shm`)) await unlink(`${dbPath}-shm`);
       copyFileSync8(restorePath, dbPath);
-      if (isCompressed && existsSync45(restorePath)) await unlink(restorePath);
+      if (isCompressed && existsSync46(restorePath)) await unlink(restorePath);
       const restoredStats = await stat3(dbPath);
       const schemaVersion = await getSchemaVersion(dbPath);
       if (options.json) {
@@ -139709,14 +139944,13 @@ function registerVerifyCommand(learning) {
   learning.command("verify").description("Verify learning database integrity").option("-f, --file <path>", "Database file to verify (defaults to current)").option("--json", "Output as JSON").action(async (options) => {
     try {
       const dbPath = options.file ? path25.resolve(options.file) : getDbPath();
-      if (!existsSync45(dbPath)) throw new Error(`Database file not found: ${dbPath}`);
+      if (!existsSync46(dbPath)) throw new Error(`Database file not found: ${dbPath}`);
       const verificationResult = await verifyDatabaseIntegrity(dbPath);
       const schemaVersion = await getSchemaVersion(dbPath);
       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();
@@ -139752,7 +139986,7 @@ function registerExportFullCommand(learning) {
   learning.command("export-full").description("Export all learning data including patterns, trajectories, and experiences").option("-o, --output <file>", "Output file path", "aqe-learning-export.json").option("--compress", "Compress output with gzip").option("--include-trajectories", "Include learning trajectories").option("--include-experiences", "Include learning experiences").option("--json", "Output as JSON (to stdout)").action(async (options) => {
     try {
       const dbPath = getDbPath();
-      if (!existsSync45(dbPath)) throw new Error('No learning database found. Run "aqe init --auto" first.');
+      if (!existsSync46(dbPath)) throw new Error('No learning database found. Run "aqe init --auto" first.');
       const reasoningBank = await initializeLearningSystem2();
       const schemaVersion = await getSchemaVersion(dbPath);
       const searchResult = await reasoningBank.searchPatterns("*", { limit: 1e4 });
@@ -139783,8 +140017,7 @@ 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();
@@ -139793,8 +140026,7 @@ 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();
@@ -139833,7 +140065,7 @@ function registerImportMergeCommand(learning) {
   learning.command("import-merge").description("Import and merge patterns from export file (preserves existing data)").requiredOption("-i, --input <file>", "Input file path").option("--skip-duplicates", "Skip patterns with matching names (default: update)").option("--dry-run", "Show what would be imported without making changes").option("--json", "Output as JSON").action(async (options) => {
     try {
       let inputPath = path25.resolve(options.input);
-      if (!existsSync45(inputPath)) throw new Error(`File not found: ${inputPath}`);
+      if (!existsSync46(inputPath)) throw new Error(`File not found: ${inputPath}`);
       let content;
       if (inputPath.endsWith(".gz")) {
         const tempPath = inputPath.replace(".gz", ".tmp.json");
@@ -140115,8 +140347,8 @@ function registerDreamCommand(learning) {
 // src/cli/commands/mcp.ts
 import { Command as Command17 } from "commander";
 import { spawn as spawn7 } from "child_process";
-import { join as join44, dirname as dirname14 } from "path";
-import { existsSync as existsSync46 } from "fs";
+import { join as join45, dirname as dirname14 } from "path";
+import { existsSync as existsSync47 } from "fs";
 import { fileURLToPath as fileURLToPath7 } from "url";
 function createMcpCommand() {
   const cmd = new Command17("mcp").description("Start the MCP protocol server for Claude Code integration").option("--http <port>", "Also start HTTP server for AG-UI/A2A protocols", "0").option("--verbose", "Enable verbose logging").action(async (options) => {
@@ -140158,17 +140390,17 @@ function findMcpEntry() {
   const __dirname5 = dirname14(__filename5);
   const candidates = [
     // 1. Bundled dist (production)
-    join44(__dirname5, "..", "..", "mcp", "bundle.js"),
+    join45(__dirname5, "..", "..", "mcp", "bundle.js"),
     // 2. Compiled dist
-    join44(__dirname5, "..", "..", "mcp", "entry.js"),
+    join45(__dirname5, "..", "..", "mcp", "entry.js"),
     // 3. Source (development with tsx)
-    join44(__dirname5, "..", "..", "mcp", "entry.ts"),
+    join45(__dirname5, "..", "..", "mcp", "entry.ts"),
     // 4. From node_modules (when used as dependency)
-    join44(process.cwd(), "node_modules", "agentic-qe", "v3", "dist", "mcp", "bundle.js"),
-    join44(process.cwd(), "node_modules", "agentic-qe", "v3", "dist", "mcp", "entry.js")
+    join45(process.cwd(), "node_modules", "agentic-qe", "v3", "dist", "mcp", "bundle.js"),
+    join45(process.cwd(), "node_modules", "agentic-qe", "v3", "dist", "mcp", "entry.js")
   ];
   for (const candidate of candidates) {
-    if (existsSync46(candidate)) {
+    if (existsSync47(candidate)) {
       return candidate;
     }
   }
@@ -140290,7 +140522,7 @@ async function cleanupAndExit(code = 0) {
   process.exit(code);
 }
 var program = new Command18();
-var VERSION = true ? "3.6.10" : "0.0.0-dev";
+var VERSION = true ? "3.6.12" : "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);