agentic-qe 3.5.2 → 3.5.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agentic-qe",
-  "version": "3.5.2",
+  "version": "3.5.3",
   "description": "Agentic Quality Engineering V3 - Domain-Driven Design Architecture with 12 Bounded Contexts, O(log n) coverage analysis, ReasoningBank learning, 51 specialized QE agents, mathematical Coherence verification, deep Claude Flow integration",
   "main": "./v3/dist/index.js",
   "types": "./v3/dist/index.d.ts",

package/v3/dist/cli/bundle.js

@@ -106315,6 +106315,8 @@ var MCPPhase = class extends BasePhase {
 };
 
 // src/init/phases/09-assets.ts
+import { existsSync as existsSync25, readFileSync as readFileSync18 } from "fs";
+import { join as join27 } from "path";
 var AssetsPhase = class extends BasePhase {
   name = "assets";
   description = "Install skills and agents";
@@ -106324,13 +106326,16 @@ var AssetsPhase = class extends BasePhase {
   async run(context2) {
     const config = context2.config;
     const { projectRoot, options } = context2;
-    const shouldOverwrite = options.upgrade || config.skills.overwrite;
+    const isVersionUpgrade = this.detectVersionUpgrade(context2);
+    const shouldOverwrite = options.upgrade || config.skills.overwrite || options.autoMode && isVersionUpgrade;
     let skillsInstalled = 0;
     let agentsInstalled = 0;
     let n8nAgents = 0;
     let n8nSkills = 0;
     if (options.upgrade) {
       context2.services.log(`  Upgrade mode: overwriting existing files`);
+    } else if (options.autoMode && isVersionUpgrade) {
+      context2.services.log(`  Version upgrade detected: updating skills and agents`);
     }
     if (config.skills.install) {
       const skillsInstaller = createSkillsInstaller({
@@ -106384,11 +106389,30 @@ var AssetsPhase = class extends BasePhase {
       n8nSkills
     };
   }
+  /**
+   * Detect if this is a version upgrade by comparing existing config version
+   * with the new version being installed
+   */
+  detectVersionUpgrade(context2) {
+    const configPath = join27(context2.projectRoot, ".agentic-qe", "config.yaml");
+    if (!existsSync25(configPath)) {
+      return false;
+    }
+    try {
+      const content = readFileSync18(configPath, "utf-8");
+      const versionMatch = content.match(/version:\s*"?([^"\n]+)"?/);
+      const existingVersion = versionMatch?.[1];
+      const newVersion = context2.config.version;
+      return existingVersion !== void 0 && existingVersion !== newVersion;
+    } catch {
+      return false;
+    }
+  }
 };
 
 // src/init/phases/10-workers.ts
-import { existsSync as existsSync25, mkdirSync as mkdirSync13, writeFileSync as writeFileSync9, readFileSync as readFileSync18 } from "fs";
-import { join as join27 } from "path";
+import { existsSync as existsSync26, mkdirSync as mkdirSync13, writeFileSync as writeFileSync9, readFileSync as readFileSync19 } from "fs";
+import { join as join28 } from "path";
 import { spawn as spawn5 } from "child_process";
 var WorkersPhase = class extends BasePhase {
   name = "workers";
@@ -106412,8 +106436,8 @@ var WorkersPhase = class extends BasePhase {
         daemonPid: null
       };
     }
-    const workersDir = join27(projectRoot, ".agentic-qe", "workers");
-    if (!existsSync25(workersDir)) {
+    const workersDir = join28(projectRoot, ".agentic-qe", "workers");
+    if (!existsSync26(workersDir)) {
       mkdirSync13(workersDir, { recursive: true });
     }
     const defaultIntervals = {
@@ -106464,7 +106488,7 @@ var WorkersPhase = class extends BasePhase {
         status: "pending"
       };
     }
-    const registryPath = join27(workersDir, "registry.json");
+    const registryPath = join28(workersDir, "registry.json");
     const registryData = {
       version: config.version,
       maxConcurrent: config.workers.maxConcurrent,
@@ -106474,18 +106498,18 @@ var WorkersPhase = class extends BasePhase {
     };
     writeFileSync9(registryPath, JSON.stringify(registryData, null, 2), "utf-8");
     for (const workerName of config.workers.enabled) {
-      const workerConfigPath = join27(workersDir, `${workerName}.json`);
+      const workerConfigPath = join28(workersDir, `${workerName}.json`);
       const workerConfig = {
         name: workerName,
         enabled: true,
         interval: config.workers.intervals[workerName] || defaultIntervals[workerName] || 6e4,
         projectRoot,
-        dataDir: join27(projectRoot, ".agentic-qe", "data"),
+        dataDir: join28(projectRoot, ".agentic-qe", "data"),
         createdAt: (/* @__PURE__ */ new Date()).toISOString()
       };
       writeFileSync9(workerConfigPath, JSON.stringify(workerConfig, null, 2), "utf-8");
     }
-    const daemonScriptPath = join27(workersDir, "start-daemon.sh");
+    const daemonScriptPath = join28(workersDir, "start-daemon.sh");
     const daemonScript = `#!/bin/bash
 # AQE v3 Worker Daemon Startup Script
 # Generated by aqe init
@@ -106553,7 +106577,7 @@ echo "To stop: kill $DAEMON_PID"
 echo "To view logs: tail -f $LOG_FILE"
 `;
     writeFileSync9(daemonScriptPath, daemonScript, { mode: 493 });
-    const stopScriptPath = join27(workersDir, "stop-daemon.sh");
+    const stopScriptPath = join28(workersDir, "stop-daemon.sh");
     const stopScript = `#!/bin/bash
 # AQE v3 Worker Daemon Stop Script
 # Generated by aqe init
@@ -106595,11 +106619,12 @@ fi
         if (daemonStarted) {
           context2.services.log(`  MCP daemon started (PID: ${daemonPid})`);
         } else if (daemonError) {
-          context2.services.log(`  MCP daemon failed: ${daemonError}`);
+          context2.services.log(`  MCP daemon: skipped (will start via Claude Code)`);
+          context2.services.log(`    Note: ${daemonError}`);
         }
       } catch (error) {
         daemonError = error instanceof Error ? error.message : "Unknown error";
-        context2.services.log(`  MCP daemon error: ${daemonError}`);
+        context2.services.log(`  MCP daemon: skipped (Claude Code will start it)`);
       }
     }
     return {
@@ -106615,11 +106640,11 @@ fi
    * Start the MCP daemon in the background
    */
   async startDaemon(workersDir, projectRoot, context2) {
-    const pidFile = join27(workersDir, "daemon.pid");
-    const logFile = join27(workersDir, "daemon.log");
-    if (existsSync25(pidFile)) {
+    const pidFile = join28(workersDir, "daemon.pid");
+    const logFile = join28(workersDir, "daemon.log");
+    if (existsSync26(pidFile)) {
       try {
-        const existingPid = parseInt(readFileSync18(pidFile, "utf-8").trim(), 10);
+        const existingPid = parseInt(readFileSync19(pidFile, "utf-8").trim(), 10);
         process.kill(existingPid, 0);
         return { started: true, pid: existingPid, error: "Already running" };
       } catch {
@@ -106708,16 +106733,16 @@ fi
    * 4. npx fallback (uses aqe mcp subcommand)
    */
   async findMcpCommand(projectRoot) {
-    const localMcpBin = join27(projectRoot, "node_modules", ".bin", "aqe-mcp");
-    if (existsSync25(localMcpBin)) {
+    const localMcpBin = join28(projectRoot, "node_modules", ".bin", "aqe-mcp");
+    if (existsSync26(localMcpBin)) {
       return { command: localMcpBin, args: [] };
     }
-    const localBundle = join27(projectRoot, "node_modules", "agentic-qe", "v3", "dist", "mcp", "bundle.js");
-    if (existsSync25(localBundle)) {
+    const localBundle = join28(projectRoot, "node_modules", "agentic-qe", "v3", "dist", "mcp", "bundle.js");
+    if (existsSync26(localBundle)) {
       return { command: "node", args: [localBundle] };
     }
-    const localAqeBin = join27(projectRoot, "node_modules", ".bin", "aqe");
-    if (existsSync25(localAqeBin)) {
+    const localAqeBin = join28(projectRoot, "node_modules", ".bin", "aqe");
+    if (existsSync26(localAqeBin)) {
       return { command: localAqeBin, args: ["mcp"] };
     }
     return { command: "npx", args: ["--yes", "agentic-qe", "mcp"] };
@@ -106725,8 +106750,8 @@ fi
 };
 
 // src/init/phases/11-claude-md.ts
-import { existsSync as existsSync26, readFileSync as readFileSync19, writeFileSync as writeFileSync10 } from "fs";
-import { join as join28 } from "path";
+import { existsSync as existsSync27, readFileSync as readFileSync20, writeFileSync as writeFileSync10 } from "fs";
+import { join as join29 } from "path";
 var ClaudeMdPhase = class extends BasePhase {
   name = "claude-md";
   description = "Generate CLAUDE.md";
@@ -106736,16 +106761,16 @@ var ClaudeMdPhase = class extends BasePhase {
   async run(context2) {
     const config = context2.config;
     const { projectRoot } = context2;
-    const claudeMdPath = join28(projectRoot, "CLAUDE.md");
+    const claudeMdPath = join29(projectRoot, "CLAUDE.md");
     const content = this.generateContent(config);
     let backupCreated = false;
-    if (existsSync26(claudeMdPath)) {
-      const existing = readFileSync19(claudeMdPath, "utf-8");
+    if (existsSync27(claudeMdPath)) {
+      const existing = readFileSync20(claudeMdPath, "utf-8");
       if (existing.includes("## Agentic QE v3")) {
         context2.services.log("  CLAUDE.md already has AQE section");
         return { generated: false, path: claudeMdPath, backupCreated: false };
       }
-      const backupPath = join28(projectRoot, "CLAUDE.md.backup");
+      const backupPath = join29(projectRoot, "CLAUDE.md.backup");
       writeFileSync10(backupPath, existing, "utf-8");
       backupCreated = true;
       writeFileSync10(claudeMdPath, existing + "\n\n" + content, "utf-8");
@@ -106857,8 +106882,8 @@ Task({ prompt: "Security audit", subagent_type: "qe-security-scanner", run_in_ba
 };
 
 // src/init/phases/12-verification.ts
-import { existsSync as existsSync27, readFileSync as readFileSync20 } from "fs";
-import { join as join29, dirname as dirname9 } from "path";
+import { existsSync as existsSync28, readFileSync as readFileSync21 } from "fs";
+import { join as join30, dirname as dirname9 } from "path";
 import { mkdirSync as mkdirSync14, writeFileSync as writeFileSync11 } from "fs";
 import { createRequire as createRequire3 } from "module";
 var require4 = createRequire3(import.meta.url);
@@ -106872,20 +106897,20 @@ var VerificationPhase = class extends BasePhase {
     const config = context2.config;
     const { projectRoot } = context2;
     const checks = [];
-    const dbPath = join29(projectRoot, ".agentic-qe", "memory.db");
+    const dbPath = join30(projectRoot, ".agentic-qe", "memory.db");
     checks.push({
       name: "Database exists",
-      passed: existsSync27(dbPath)
+      passed: existsSync28(dbPath)
     });
     checks.push({
       name: ".agentic-qe directory",
-      passed: existsSync27(join29(projectRoot, ".agentic-qe"))
+      passed: existsSync28(join30(projectRoot, ".agentic-qe"))
     });
-    const configPath = join29(projectRoot, ".agentic-qe", "config.yaml");
+    const configPath = join30(projectRoot, ".agentic-qe", "config.yaml");
     await this.saveConfig(config, projectRoot);
     checks.push({
       name: "Config saved",
-      passed: existsSync27(configPath)
+      passed: existsSync28(configPath)
     });
     const versionWritten = await this.writeVersionToDb(config.version, projectRoot);
     checks.push({
@@ -106896,12 +106921,15 @@ var VerificationPhase = class extends BasePhase {
     const allCriticalPassed = checks.filter((c2) => criticalChecks.includes(c2.name)).every((c2) => c2.passed);
     context2.services.log("  Verification checks:");
     for (const check of checks) {
-      context2.services.log(`    ${check.passed ? "\u2713" : "\u2717"} ${check.name}`);
+      const isCritical = criticalChecks.includes(check.name);
+      const icon = check.passed ? "\u2713" : isCritical ? "\u2717" : "\u26A0";
+      const suffix = !isCritical && !check.passed ? " (optional)" : "";
+      context2.services.log(`    ${icon} ${check.name}${suffix}`);
     }
     return {
       verified: allCriticalPassed,
       versionWritten,
-      configSaved: existsSync27(configPath),
+      configSaved: existsSync28(configPath),
       checks
     };
   }
@@ -106909,10 +106937,10 @@ var VerificationPhase = class extends BasePhase {
    * Write AQE version to memory.db
    */
   async writeVersionToDb(version, projectRoot) {
-    const memoryDbPath = join29(projectRoot, ".agentic-qe", "memory.db");
+    const memoryDbPath = join30(projectRoot, ".agentic-qe", "memory.db");
     try {
       const dir = dirname9(memoryDbPath);
-      if (!existsSync27(dir)) {
+      if (!existsSync28(dir)) {
         mkdirSync14(dir, { recursive: true });
       }
       const Database8 = require4("better-sqlite3");
@@ -106952,12 +106980,12 @@ var VerificationPhase = class extends BasePhase {
    * Preserves user customizations from existing config (Issue #206)
    */
   async saveConfig(config, projectRoot) {
-    const configDir = join29(projectRoot, ".agentic-qe");
-    if (!existsSync27(configDir)) {
+    const configDir = join30(projectRoot, ".agentic-qe");
+    if (!existsSync28(configDir)) {
       mkdirSync14(configDir, { recursive: true });
     }
-    const configPath = join29(configDir, "config.yaml");
-    if (existsSync27(configPath)) {
+    const configPath = join30(configDir, "config.yaml");
+    if (existsSync28(configPath)) {
       const existingConfig = this.loadExistingConfig(configPath);
       if (existingConfig) {
         config = this.mergeConfigs(config, existingConfig);
@@ -106972,7 +107000,7 @@ var VerificationPhase = class extends BasePhase {
    */
   loadExistingConfig(configPath) {
     try {
-      const content = readFileSync20(configPath, "utf-8");
+      const content = readFileSync21(configPath, "utf-8");
       return this.parseYAML(content);
     } catch {
       return null;
@@ -107180,18 +107208,18 @@ var VerificationPhase = class extends BasePhase {
 };
 
 // src/init/governance-installer.ts
-import { existsSync as existsSync28, mkdirSync as mkdirSync15, readdirSync as readdirSync9, copyFileSync as copyFileSync6 } from "fs";
-import { join as join30, dirname as dirname10 } from "path";
+import { existsSync as existsSync29, mkdirSync as mkdirSync15, readdirSync as readdirSync9, copyFileSync as copyFileSync6 } from "fs";
+import { join as join31, dirname as dirname10 } from "path";
 import { fileURLToPath as fileURLToPath4 } from "url";
 var __filename3 = fileURLToPath4(import.meta.url);
 var __dirname3 = dirname10(__filename3);
 function getGovernanceAssetsPath() {
-  const devPath = join30(__dirname3, "../../assets/governance");
-  const prodPath = join30(__dirname3, "../assets/governance");
-  if (existsSync28(devPath)) return devPath;
-  if (existsSync28(prodPath)) return prodPath;
-  const fallbackPath = join30(process.cwd(), "v3/assets/governance");
-  if (existsSync28(fallbackPath)) return fallbackPath;
+  const devPath = join31(__dirname3, "../../assets/governance");
+  const prodPath = join31(__dirname3, "../assets/governance");
+  if (existsSync29(devPath)) return devPath;
+  if (existsSync29(prodPath)) return prodPath;
+  const fallbackPath = join31(process.cwd(), "v3/assets/governance");
+  if (existsSync29(fallbackPath)) return fallbackPath;
   throw new Error("Governance assets not found. Package may be corrupted.");
 }
 var GovernanceInstaller = class {
@@ -107212,8 +107240,8 @@ var GovernanceInstaller = class {
     const installed = [];
     const skipped = [];
     const errors = [];
-    const governanceDir = join30(this.projectRoot, ".claude", "guidance");
-    const shardsDir = join30(governanceDir, "shards");
+    const governanceDir = join31(this.projectRoot, ".claude", "guidance");
+    const shardsDir = join31(governanceDir, "shards");
     try {
       mkdirSync15(governanceDir, { recursive: true });
       if (!this.skipShards) {
@@ -107231,11 +107259,11 @@ var GovernanceInstaller = class {
       };
     }
     let constitutionInstalled = false;
-    const constitutionSrc = join30(this.assetsPath, "constitution.md");
-    const constitutionDest = join30(governanceDir, "constitution.md");
-    if (existsSync28(constitutionSrc)) {
+    const constitutionSrc = join31(this.assetsPath, "constitution.md");
+    const constitutionDest = join31(governanceDir, "constitution.md");
+    if (existsSync29(constitutionSrc)) {
       try {
-        if (!existsSync28(constitutionDest) || this.overwrite) {
+        if (!existsSync29(constitutionDest) || this.overwrite) {
           copyFileSync6(constitutionSrc, constitutionDest);
           installed.push("constitution.md");
           constitutionInstalled = true;
@@ -107250,15 +107278,15 @@ var GovernanceInstaller = class {
     }
     let shardsInstalled = 0;
     if (!this.skipShards) {
-      const shardsSrcDir = join30(this.assetsPath, "shards");
-      if (existsSync28(shardsSrcDir)) {
+      const shardsSrcDir = join31(this.assetsPath, "shards");
+      if (existsSync29(shardsSrcDir)) {
         try {
           const shardFiles = readdirSync9(shardsSrcDir).filter((f3) => f3.endsWith(".shard.md"));
           for (const shardFile of shardFiles) {
-            const shardSrc = join30(shardsSrcDir, shardFile);
-            const shardDest = join30(shardsDir, shardFile);
+            const shardSrc = join31(shardsSrcDir, shardFile);
+            const shardDest = join31(shardsDir, shardFile);
             try {
-              if (!existsSync28(shardDest) || this.overwrite) {
+              if (!existsSync29(shardDest) || this.overwrite) {
                 copyFileSync6(shardSrc, shardDest);
                 installed.push(`shards/${shardFile}`);
                 shardsInstalled++;
@@ -107289,15 +107317,15 @@ var GovernanceInstaller = class {
    * Check if governance is already installed
    */
   isInstalled() {
-    const constitutionPath = join30(this.projectRoot, ".claude", "guidance", "constitution.md");
-    return existsSync28(constitutionPath);
+    const constitutionPath = join31(this.projectRoot, ".claude", "guidance", "constitution.md");
+    return existsSync29(constitutionPath);
   }
   /**
    * Get list of installed shards
    */
   getInstalledShards() {
-    const shardsDir = join30(this.projectRoot, ".claude", "guidance", "shards");
-    if (!existsSync28(shardsDir)) return [];
+    const shardsDir = join31(this.projectRoot, ".claude", "guidance", "shards");
+    if (!existsSync29(shardsDir)) return [];
     try {
       return readdirSync9(shardsDir).filter((f3) => f3.endsWith(".shard.md"));
     } catch {
@@ -107576,14 +107604,14 @@ function createModularInitOrchestrator(options) {
 }
 
 // src/cli/commands/claude-flow-setup.ts
-import { existsSync as existsSync29, writeFileSync as writeFileSync13, readFileSync as readFileSync22 } from "node:fs";
-import { join as join31 } from "node:path";
+import { existsSync as existsSync30, writeFileSync as writeFileSync13, readFileSync as readFileSync23 } from "node:fs";
+import { join as join32 } from "node:path";
 import { execSync as execSync6 } from "node:child_process";
 async function detectClaudeFlow(projectRoot, debug) {
-  const claudeSettingsPath = join31(projectRoot, ".claude", "settings.json");
-  if (existsSync29(claudeSettingsPath)) {
+  const claudeSettingsPath = join32(projectRoot, ".claude", "settings.json");
+  if (existsSync30(claudeSettingsPath)) {
     try {
-      const settings = JSON.parse(readFileSync22(claudeSettingsPath, "utf-8"));
+      const settings = JSON.parse(readFileSync23(claudeSettingsPath, "utf-8"));
       const mcpServers = settings.mcpServers || settings.mcp?.servers || {};
       if (mcpServers["claude-flow"] || mcpServers["@anthropic/claude-flow"]) {
         if (debug) console.log("[ClaudeFlow] Detected via MCP settings");
@@ -107604,9 +107632,9 @@ async function detectClaudeFlow(projectRoot, debug) {
   } catch {
   }
   try {
-    const packageJsonPath = join31(projectRoot, "package.json");
-    if (existsSync29(packageJsonPath)) {
-      const pkg = JSON.parse(readFileSync22(packageJsonPath, "utf-8"));
+    const packageJsonPath = join32(projectRoot, "package.json");
+    if (existsSync30(packageJsonPath)) {
+      const pkg = JSON.parse(readFileSync23(packageJsonPath, "utf-8"));
       const deps = { ...pkg.dependencies, ...pkg.devDependencies };
       if (deps["@claude-flow/cli"] || deps["claude-flow"]) {
         if (debug) console.log("[ClaudeFlow] Detected via package.json");
@@ -107686,11 +107714,11 @@ function generateClaudeFlowConfig(projectRoot, features) {
   };
 }
 function updateMCPConfig(projectRoot) {
-  const claudeSettingsPath = join31(projectRoot, ".claude", "settings.json");
+  const claudeSettingsPath = join32(projectRoot, ".claude", "settings.json");
   let settings = {};
-  if (existsSync29(claudeSettingsPath)) {
+  if (existsSync30(claudeSettingsPath)) {
     try {
-      settings = JSON.parse(readFileSync22(claudeSettingsPath, "utf-8"));
+      settings = JSON.parse(readFileSync23(claudeSettingsPath, "utf-8"));
     } catch {
     }
   }
@@ -107746,8 +107774,8 @@ async function setupClaudeFlowIntegration(options) {
       features
     };
   }
-  const aqeDir = join31(projectRoot, ".agentic-qe");
-  const configPath = join31(aqeDir, "claude-flow-integration.json");
+  const aqeDir = join32(projectRoot, ".agentic-qe");
+  const configPath = join32(aqeDir, "claude-flow-integration.json");
   try {
     const config = generateClaudeFlowConfig(projectRoot, features);
     writeFileSync13(configPath, JSON.stringify(config, null, 2));
@@ -108233,8 +108261,8 @@ import cliProgress, { MultiBar, Presets } from "cli-progress";
 import ora from "ora";
 
 // src/cli/config/cli-config.ts
-import { existsSync as existsSync30, readFileSync as readFileSync23, writeFileSync as writeFileSync14, mkdirSync as mkdirSync16, unlinkSync as unlinkSync3 } from "fs";
-import { join as join32 } from "path";
+import { existsSync as existsSync31, readFileSync as readFileSync24, writeFileSync as writeFileSync14, mkdirSync as mkdirSync16, unlinkSync as unlinkSync3 } from "fs";
+import { join as join33 } from "path";
 import { homedir as homedir2 } from "os";
 var DEFAULT_CLI_CONFIG = {
   wizards: {
@@ -108261,10 +108289,10 @@ var DEFAULT_CLI_CONFIG = {
   }
 };
 function getConfigDir() {
-  return join32(homedir2(), ".aqe");
+  return join33(homedir2(), ".aqe");
 }
 function getConfigPath() {
-  return join32(getConfigDir(), "cli-config.json");
+  return join33(getConfigDir(), "cli-config.json");
 }
 var cachedConfig = null;
 var cacheTimestamp = 0;
@@ -108418,11 +108446,11 @@ function deepMerge(target, source) {
 }
 function loadCLIConfig() {
   const configPath = getConfigPath();
-  if (!existsSync30(configPath)) {
+  if (!existsSync31(configPath)) {
     return { ...DEFAULT_CLI_CONFIG };
   }
   try {
-    const content = readFileSync23(configPath, "utf-8");
+    const content = readFileSync24(configPath, "utf-8");
     const parsed = JSON.parse(content);
     const validation = validateConfig(parsed);
     if (!validation.valid) {
@@ -109446,12 +109474,12 @@ var BaseWizardCommand = class {
 };
 
 // src/cli/wizards/core/wizard-step.ts
-import { existsSync as existsSync32 } from "fs";
+import { existsSync as existsSync33 } from "fs";
 import { resolve as resolve7 } from "path";
 
 // src/cli/wizards/core/wizard-utils.ts
-import { existsSync as existsSync31, statSync as statSync8 } from "fs";
-import { join as join33, relative as relative6 } from "path";
+import { existsSync as existsSync32, statSync as statSync8 } from "fs";
+import { join as join34, relative as relative6 } from "path";
 var WizardPrompt = class {
   /**
    * Generic prompt helper - wraps readline.question in a Promise
@@ -109542,8 +109570,8 @@ var WizardSuggestions = class _WizardSuggestions {
     const suggestions = [];
     const commonDirs = ["src", "lib", "app", "packages", "api"];
     for (const dir of commonDirs) {
-      const dirPath = join33(cwd, dir);
-      if (existsSync31(dirPath) && statSync8(dirPath).isDirectory()) {
+      const dirPath = join34(cwd, dir);
+      if (existsSync32(dirPath) && statSync8(dirPath).isDirectory()) {
         suggestions.push(dir);
       }
     }
@@ -109561,8 +109589,8 @@ var WizardSuggestions = class _WizardSuggestions {
       ".nyc_output"
     ];
     for (const loc of coverageLocations) {
-      const locPath = join33(cwd, loc);
-      if (existsSync31(locPath)) {
+      const locPath = join34(cwd, loc);
+      if (existsSync32(locPath)) {
         suggestions.push(loc);
       }
     }
@@ -109584,8 +109612,8 @@ var WizardSuggestions = class _WizardSuggestions {
       "Dockerfile"
     ];
     for (const file of securityFiles) {
-      const filePath = join33(cwd, file);
-      if (existsSync31(filePath)) {
+      const filePath = join34(cwd, file);
+      if (existsSync32(filePath)) {
         suggestions.push(file);
       }
     }
@@ -109598,13 +109626,13 @@ var WizardSuggestions = class _WizardSuggestions {
     const suggestions = [];
     const commonDirs = ["src", "lib", "app", "packages"];
     for (const dir of commonDirs) {
-      const dirPath = join33(cwd, dir);
-      if (existsSync31(dirPath) && statSync8(dirPath).isDirectory()) {
+      const dirPath = join34(cwd, dir);
+      if (existsSync32(dirPath) && statSync8(dirPath).isDirectory()) {
         suggestions.push(`${dir}/**/*.ts`);
         suggestions.push(dir);
       }
     }
-    if (existsSync31(join33(cwd, "src"))) {
+    if (existsSync32(join34(cwd, "src"))) {
       suggestions.push("src/services/**/*.ts");
       suggestions.push("src/utils/**/*.ts");
       suggestions.push("src/components/**/*.tsx");
@@ -109616,12 +109644,12 @@ var WizardSuggestions = class _WizardSuggestions {
    */
   static checkPatternsExist(cwd) {
     const patternLocations = [
-      join33(cwd, ".agentic-qe", "patterns"),
-      join33(cwd, ".agentic-qe", "memory.db"),
-      join33(cwd, ".aqe", "patterns"),
-      join33(cwd, "data", "patterns")
+      join34(cwd, ".agentic-qe", "patterns"),
+      join34(cwd, ".agentic-qe", "memory.db"),
+      join34(cwd, ".aqe", "patterns"),
+      join34(cwd, "data", "patterns")
     ];
-    return patternLocations.some((loc) => existsSync31(loc));
+    return patternLocations.some((loc) => existsSync32(loc));
   }
 };
 var WizardFormat = class {
@@ -109898,7 +109926,7 @@ var PathInputStep = class extends BaseWizardCommand {
   async execute(context2) {
     if (context2.nonInteractive) {
       const resolved2 = resolve7(context2.cwd, this.defaultValue);
-      return this.success(existsSync32(resolved2) ? resolved2 : context2.cwd);
+      return this.success(existsSync33(resolved2) ? resolved2 : context2.cwd);
     }
     WizardPrompt.printStepHeader(this.stepNumber, this.title, this.description);
     if (this.examples) {
@@ -109921,7 +109949,7 @@ var PathInputStep = class extends BaseWizardCommand {
     );
     const value = input.trim() || this.defaultValue;
     const resolved = resolve7(context2.cwd, value);
-    if (this.validatePath && !existsSync32(resolved)) {
+    if (this.validatePath && !existsSync33(resolved)) {
       console.log(source_default.yellow(`  Warning: '${value}' does not exist, using current directory.`));
       return this.success(context2.cwd);
     }
@@ -112973,8 +113001,8 @@ import { Command as Command8 } from "commander";
 init_types();
 
 // src/init/fleet-integration.ts
-import { existsSync as existsSync33 } from "fs";
-import { join as join35 } from "path";
+import { existsSync as existsSync34 } from "fs";
+import { join as join36 } from "path";
 var FleetInitEnhancer = class {
   projectRoot;
   options;
@@ -113086,7 +113114,7 @@ var FleetInitEnhancer = class {
       });
       console.log(source_default.gray(`  Indexing ${files.length} files...`));
       const result = await kgService.index({
-        paths: files.map((f3) => join35(this.projectRoot, f3)),
+        paths: files.map((f3) => join36(this.projectRoot, f3)),
         incremental: false,
         includeTests: true
       });
@@ -113121,8 +113149,8 @@ var FleetInitEnhancer = class {
    * Checks the memory database for code-intelligence:kg namespace entries
    */
   async hasCodeIntelligenceIndex() {
-    const dbPath = join35(this.projectRoot, ".agentic-qe", "memory.db");
-    if (!existsSync33(dbPath)) {
+    const dbPath = join36(this.projectRoot, ".agentic-qe", "memory.db");
+    if (!existsSync34(dbPath)) {
       return false;
     }
     try {
@@ -113142,7 +113170,7 @@ var FleetInitEnhancer = class {
    * Get count of knowledge graph entries
    */
   async getKGEntryCount() {
-    const dbPath = join35(this.projectRoot, ".agentic-qe", "memory.db");
+    const dbPath = join36(this.projectRoot, ".agentic-qe", "memory.db");
     try {
       const Database8 = (await import("better-sqlite3")).default;
       const db = new Database8(dbPath);
@@ -114623,7 +114651,7 @@ function createParallelEvalRunner(skillValidationLearner, config = {}, executor2
 }
 
 // src/validation/validation-result-aggregator.ts
-import { readFileSync as readFileSync25, writeFileSync as writeFileSync15, existsSync as existsSync35 } from "fs";
+import { readFileSync as readFileSync26, writeFileSync as writeFileSync15, existsSync as existsSync36 } from "fs";
 var DEFAULT_CONFIG59 = {
   varianceThreshold: 0.04,
   // ~20% standard deviation
@@ -114968,10 +114996,10 @@ var ValidationResultAggregator = class {
    * Update trust tier manifest with new pass rates
    */
   async updateManifest(report) {
-    if (!existsSync35(this.manifestPath)) {
+    if (!existsSync36(this.manifestPath)) {
       throw new Error(`Manifest file not found: ${this.manifestPath}`);
     }
-    const manifest = JSON.parse(readFileSync25(this.manifestPath, "utf-8"));
+    const manifest = JSON.parse(readFileSync26(this.manifestPath, "utf-8"));
     for (const [skillName, summary] of report.skillResults.entries()) {
       if (manifest.skills && manifest.skills[skillName]) {
         const skill = manifest.skills[skillName];
@@ -117682,20 +117710,20 @@ function formatDuration2(ms) {
 
 // src/cli/commands/validate.ts
 import { Command as Command10 } from "commander";
-import { readFileSync as readFileSync26, writeFileSync as writeFileSync16, existsSync as existsSync36, readdirSync as readdirSync10, statSync as statSync10 } from "fs";
-import { join as join37, resolve as resolve8, basename as basename7 } from "path";
+import { readFileSync as readFileSync27, writeFileSync as writeFileSync16, existsSync as existsSync37, readdirSync as readdirSync10, statSync as statSync10 } from "fs";
+import { join as join38, resolve as resolve8, basename as basename7 } from "path";
 function loadValidationResults(inputPath) {
   const resolvedPath = resolve8(inputPath);
-  if (!existsSync36(resolvedPath)) {
+  if (!existsSync37(resolvedPath)) {
     throw new Error(`Input path not found: ${resolvedPath}`);
   }
   const stat4 = statSync10(resolvedPath);
   if (stat4.isDirectory()) {
     const results = [];
-    const files = readdirSync10(resolvedPath).filter((f3) => f3.endsWith(".json")).map((f3) => join37(resolvedPath, f3));
+    const files = readdirSync10(resolvedPath).filter((f3) => f3.endsWith(".json")).map((f3) => join38(resolvedPath, f3));
     for (const file of files) {
       try {
-        const content = JSON.parse(readFileSync26(file, "utf-8"));
+        const content = JSON.parse(readFileSync27(file, "utf-8"));
         if (isValidationRunResult(content)) {
           results.push(content);
         } else if (Array.isArray(content)) {
@@ -117711,7 +117739,7 @@ function loadValidationResults(inputPath) {
     }
     return results;
   } else {
-    const content = JSON.parse(readFileSync26(resolvedPath, "utf-8"));
+    const content = JSON.parse(readFileSync27(resolvedPath, "utf-8"));
     if (isValidationRunResult(content)) {
       return [content];
     } else if (Array.isArray(content)) {
@@ -117742,15 +117770,15 @@ function createMockLearner() {
 function getDefaultManifestPath() {
   const cwd = process.cwd();
   const candidates = [
-    join37(cwd, ".claude/skills/trust-tier-manifest.json"),
-    join37(cwd, ".claude/skills/skills-manifest.json")
+    join38(cwd, ".claude/skills/trust-tier-manifest.json"),
+    join38(cwd, ".claude/skills/skills-manifest.json")
   ];
   for (const candidate of candidates) {
-    if (existsSync36(candidate)) {
+    if (existsSync37(candidate)) {
       return candidate;
     }
   }
-  return join37(cwd, ".claude/skills/trust-tier-manifest.json");
+  return join38(cwd, ".claude/skills/trust-tier-manifest.json");
 }
 function writeReport(report, aggregator, options) {
   const format = options.format || "markdown";
@@ -124809,8 +124837,8 @@ async function createCoherenceService(wasmLoader2, config, logger) {
 // src/integrations/coherence/wasm-loader.ts
 import { createRequire as createRequire4 } from "node:module";
 import { fileURLToPath as fileURLToPath6 } from "node:url";
-import { dirname as dirname13, join as join39 } from "node:path";
-import { readFileSync as readFileSync29, existsSync as existsSync39 } from "node:fs";
+import { dirname as dirname13, join as join40 } from "node:path";
+import { readFileSync as readFileSync30, existsSync as existsSync40 } from "node:fs";
 var FALLBACK_RETRY_DELAYS_MS = [1e3, 2e3, 4e3];
 var WasmLoader = class {
   state = "unloaded";
@@ -125068,15 +125096,15 @@ var WasmLoader = class {
         (() => {
           try {
             const modulePath = require5.resolve("prime-radiant-advanced-wasm");
-            return join39(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
+            return join40(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
           } catch {
             return null;
           }
         })(),
-        join39(process.cwd(), "node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm")
+        join40(process.cwd(), "node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm")
       ].filter((p3) => p3 !== null);
       for (const path23 of wasmPaths) {
-        if (existsSync39(path23)) {
+        if (existsSync40(path23)) {
           return true;
         }
       }
@@ -125327,19 +125355,19 @@ var WasmLoader = class {
       (() => {
         try {
           const modulePath = require5.resolve("prime-radiant-advanced-wasm");
-          return join39(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
+          return join40(dirname13(modulePath), "prime_radiant_advanced_wasm_bg.wasm");
         } catch {
           return null;
         }
       })(),
       // Direct node_modules path from current file
-      join39(dirname13(fileURLToPath6(import.meta.url)), "../../../../node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm"),
+      join40(dirname13(fileURLToPath6(import.meta.url)), "../../../../node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm"),
       // Workspace root
-      join39(process.cwd(), "node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm")
+      join40(process.cwd(), "node_modules/prime-radiant-advanced-wasm/prime_radiant_advanced_wasm_bg.wasm")
     ].filter((p3) => p3 !== null);
     let wasmPath = null;
     for (const path23 of wasmPaths) {
-      if (existsSync39(path23)) {
+      if (existsSync40(path23)) {
         wasmPath = path23;
         break;
       }
@@ -125351,7 +125379,7 @@ ${wasmPaths.join("\n")}
 Ensure prime-radiant-advanced-wasm is installed.`
       );
     }
-    const wasmBytes = readFileSync29(wasmPath);
+    const wasmBytes = readFileSync30(wasmPath);
     if (wasmModule.initSync && typeof wasmModule.initSync === "function") {
       wasmModule.initSync({ module: wasmBytes });
     } else {
@@ -126166,7 +126194,7 @@ Registered: ${events.length}/${Object.keys(QE_HOOK_EVENTS).length}`)
 // src/cli/commands/learning.ts
 import { Command as Command16 } from "commander";
 import path22 from "node:path";
-import { existsSync as existsSync41, writeFileSync as writeFileSync20, readFileSync as readFileSync30, mkdirSync as mkdirSync17, copyFileSync as copyFileSync7 } from "node:fs";
+import { existsSync as existsSync42, writeFileSync as writeFileSync20, readFileSync as readFileSync31, mkdirSync as mkdirSync17, copyFileSync as copyFileSync7 } from "node:fs";
 import { createReadStream, createWriteStream } from "node:fs";
 import { stat as stat3, unlink } from "node:fs/promises";
 import { createGzip, createGunzip } from "node:zlib";
@@ -126175,7 +126203,7 @@ import { pipeline as pipeline3 } from "node:stream/promises";
 // src/learning/metrics-tracker.ts
 import Database7 from "better-sqlite3";
 import path21 from "node:path";
-import { existsSync as existsSync40 } from "node:fs";
+import { existsSync as existsSync41 } from "node:fs";
 var LearningMetricsTracker = class {
   db = null;
   dbPath;
@@ -126188,7 +126216,7 @@ var LearningMetricsTracker = class {
    */
   async initialize() {
     if (this.initialized) return;
-    if (!existsSync40(this.dbPath)) {
+    if (!existsSync41(this.dbPath)) {
       throw new Error(`Database not found: ${this.dbPath}. Run "aqe init --auto" first.`);
     }
     this.db = new Database7(this.dbPath, { readonly: false });
@@ -126887,10 +126915,10 @@ Examples:
   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 = path22.resolve(options.input);
-      if (!existsSync41(inputPath)) {
+      if (!existsSync42(inputPath)) {
         throw new Error(`File not found: ${inputPath}`);
       }
-      const content = readFileSync30(inputPath, "utf-8");
+      const content = readFileSync31(inputPath, "utf-8");
       const importData = JSON.parse(content);
       if (!importData.patterns || !Array.isArray(importData.patterns)) {
         throw new Error("Invalid pattern file format");
@@ -126970,7 +126998,7 @@ Examples:
       }
       console.log(source_default.bold("\n\u{1F5D1}\uFE0F  Resetting Learning Data\n"));
       for (const file of filesToReset) {
-        if (existsSync41(file)) {
+        if (existsSync42(file)) {
           console.log(source_default.dim(`  Removing: ${path22.relative(cwd, file)}`));
         }
       }
@@ -126986,7 +127014,7 @@ Examples:
     try {
       const cwd = process.cwd();
       const dbPath = path22.join(cwd, ".agentic-qe", "memory.db");
-      if (!existsSync41(dbPath)) {
+      if (!existsSync42(dbPath)) {
         throw new Error('No memory database found. Run "aqe init --auto" first.');
       }
       const minReward = parseFloat(options.minReward);
@@ -127242,28 +127270,28 @@ Examples:
   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 (!existsSync41(dbPath)) {
+      if (!existsSync42(dbPath)) {
         throw new Error(`No learning database found at: ${dbPath}`);
       }
       const timestamp = (/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, 19);
       const defaultOutput = path22.join(process.cwd(), "backups", `learning-${timestamp}.db`);
       let outputPath = options.output ? path22.resolve(options.output) : defaultOutput;
       const backupDir = path22.dirname(outputPath);
-      if (!existsSync41(backupDir)) {
+      if (!existsSync42(backupDir)) {
         mkdirSync17(backupDir, { recursive: true });
       }
       const sourceStats = await stat3(dbPath);
       const sourceSizeKB = (sourceStats.size / 1024).toFixed(2);
       copyFileSync7(dbPath, outputPath);
       const walPath = `${dbPath}-wal`;
-      if (existsSync41(walPath)) {
+      if (existsSync42(walPath)) {
         copyFileSync7(walPath, `${outputPath}-wal`);
       }
       let finalPath = outputPath;
       if (options.compress) {
         finalPath = await compressFile(outputPath);
         await unlink(outputPath);
-        if (existsSync41(`${outputPath}-wal`)) {
+        if (existsSync42(`${outputPath}-wal`)) {
           await unlink(`${outputPath}-wal`);
         }
       }
@@ -127317,7 +127345,7 @@ Examples:
     try {
       const inputPath = path22.resolve(options.input);
       const dbPath = getDbPath();
-      if (!existsSync41(inputPath)) {
+      if (!existsSync42(inputPath)) {
         throw new Error(`Backup file not found: ${inputPath}`);
       }
       const isCompressed = inputPath.endsWith(".gz");
@@ -127330,35 +127358,35 @@ Examples:
       if (options.verify) {
         const verificationResult = await verifyDatabaseIntegrity(restorePath);
         if (!verificationResult.valid) {
-          if (isCompressed && existsSync41(restorePath)) {
+          if (isCompressed && existsSync42(restorePath)) {
             await unlink(restorePath);
           }
           throw new Error(`Backup verification failed: ${verificationResult.message}`);
         }
       }
-      if (existsSync41(dbPath) && !options.force) {
+      if (existsSync42(dbPath) && !options.force) {
         printError2(`Database already exists at: ${dbPath}`);
         console.log(source_default.yellow("  Use --force to overwrite"));
-        if (isCompressed && existsSync41(restorePath)) {
+        if (isCompressed && existsSync42(restorePath)) {
           await unlink(restorePath);
         }
         process.exit(1);
       }
       const targetDir = path22.dirname(dbPath);
-      if (!existsSync41(targetDir)) {
+      if (!existsSync42(targetDir)) {
         mkdirSync17(targetDir, { recursive: true });
       }
-      if (existsSync41(dbPath)) {
+      if (existsSync42(dbPath)) {
         await unlink(dbPath);
       }
-      if (existsSync41(`${dbPath}-wal`)) {
+      if (existsSync42(`${dbPath}-wal`)) {
         await unlink(`${dbPath}-wal`);
       }
-      if (existsSync41(`${dbPath}-shm`)) {
+      if (existsSync42(`${dbPath}-shm`)) {
         await unlink(`${dbPath}-shm`);
       }
       copyFileSync7(restorePath, dbPath);
-      if (isCompressed && existsSync41(restorePath)) {
+      if (isCompressed && existsSync42(restorePath)) {
         await unlink(restorePath);
       }
       const restoredStats = await stat3(dbPath);
@@ -127391,7 +127419,7 @@ Examples:
   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 ? path22.resolve(options.file) : getDbPath();
-      if (!existsSync41(dbPath)) {
+      if (!existsSync42(dbPath)) {
         throw new Error(`Database file not found: ${dbPath}`);
       }
       const verificationResult = await verifyDatabaseIntegrity(dbPath);
@@ -127449,7 +127477,7 @@ Examples:
   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 (!existsSync41(dbPath)) {
+      if (!existsSync42(dbPath)) {
         throw new Error('No learning database found. Run "aqe init --auto" first.');
       }
       const reasoningBank = await initializeLearningSystem();
@@ -127564,17 +127592,17 @@ Examples:
   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 = path22.resolve(options.input);
-      if (!existsSync41(inputPath)) {
+      if (!existsSync42(inputPath)) {
         throw new Error(`File not found: ${inputPath}`);
       }
       let content;
       if (inputPath.endsWith(".gz")) {
         const tempPath = inputPath.replace(".gz", ".tmp.json");
         await decompressFile(inputPath, tempPath);
-        content = readFileSync30(tempPath, "utf-8");
+        content = readFileSync31(tempPath, "utf-8");
         await unlink(tempPath);
       } else {
-        content = readFileSync30(inputPath, "utf-8");
+        content = readFileSync31(inputPath, "utf-8");
       }
       const importData = JSON.parse(content);
       if (!importData.patterns || !Array.isArray(importData.patterns)) {
@@ -127684,8 +127712,8 @@ Examples:
 // src/cli/commands/mcp.ts
 import { Command as Command17 } from "commander";
 import { spawn as spawn7 } from "child_process";
-import { join as join40, dirname as dirname14 } from "path";
-import { existsSync as existsSync42 } from "fs";
+import { join as join41, dirname as dirname14 } from "path";
+import { existsSync as existsSync43 } 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) => {
@@ -127727,17 +127755,17 @@ function findMcpEntry() {
   const __dirname5 = dirname14(__filename5);
   const candidates = [
     // 1. Bundled dist (production)
-    join40(__dirname5, "..", "..", "mcp", "bundle.js"),
+    join41(__dirname5, "..", "..", "mcp", "bundle.js"),
     // 2. Compiled dist
-    join40(__dirname5, "..", "..", "mcp", "entry.js"),
+    join41(__dirname5, "..", "..", "mcp", "entry.js"),
     // 3. Source (development with tsx)
-    join40(__dirname5, "..", "..", "mcp", "entry.ts"),
+    join41(__dirname5, "..", "..", "mcp", "entry.ts"),
     // 4. From node_modules (when used as dependency)
-    join40(process.cwd(), "node_modules", "agentic-qe", "v3", "dist", "mcp", "bundle.js"),
-    join40(process.cwd(), "node_modules", "agentic-qe", "v3", "dist", "mcp", "entry.js")
+    join41(process.cwd(), "node_modules", "agentic-qe", "v3", "dist", "mcp", "bundle.js"),
+    join41(process.cwd(), "node_modules", "agentic-qe", "v3", "dist", "mcp", "entry.js")
   ];
   for (const candidate of candidates) {
-    if (existsSync42(candidate)) {
+    if (existsSync43(candidate)) {
       return candidate;
     }
   }
@@ -127859,7 +127887,7 @@ async function cleanupAndExit(code = 0) {
   process.exit(code);
 }
 var program = new Command18();
-var VERSION = true ? "3.5.2" : "0.0.0-dev";
+var VERSION = true ? "3.5.3" : "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);

package/v3/dist/init/phases/09-assets.d.ts

@@ -19,5 +19,10 @@ export declare class AssetsPhase extends BasePhase<AssetsResult> {
     readonly critical = false;
     readonly requiresPhases: readonly ["configuration"];
     protected run(context: InitContext): Promise<AssetsResult>;
+    /**
+     * Detect if this is a version upgrade by comparing existing config version
+     * with the new version being installed
+     */
+    private detectVersionUpgrade;
 }
 //# sourceMappingURL=09-assets.d.ts.map

package/v3/dist/init/phases/09-assets.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"09-assets.d.ts","sourceRoot":"","sources":["../../../src/init/phases/09-assets.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,OAAO,EACL,SAAS,EACT,KAAK,WAAW,EACjB,MAAM,sBAAsB,CAAC;AAM9B,MAAM,WAAW,YAAY;IAC3B,eAAe,EAAE,MAAM,CAAC;IACxB,eAAe,EAAE,MAAM,CAAC;IACxB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;GAEG;AACH,qBAAa,WAAY,SAAQ,SAAS,CAAC,YAAY,CAAC;IACtD,QAAQ,CAAC,IAAI,YAAY;IACzB,QAAQ,CAAC,WAAW,+BAA+B;IACnD,QAAQ,CAAC,KAAK,MAAM;IACpB,QAAQ,CAAC,QAAQ,SAAS;IAC1B,QAAQ,CAAC,cAAc,6BAA8B;cAErC,GAAG,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,CAAC;IAwFhE;;;OAGG;IACH,OAAO,CAAC,oBAAoB;CAkB7B"}

package/v3/dist/init/phases/09-assets.js

@@ -2,6 +2,8 @@
  * Phase 09: Assets
  * Installs skills and agents
  */
+import { existsSync, readFileSync } from 'fs';
+import { join } from 'path';
 import { BasePhase, } from './phase-interface.js';
 import { createSkillsInstaller } from '../skills-installer.js';
 import { createAgentsInstaller } from '../agents-installer.js';
@@ -18,8 +20,11 @@ export class AssetsPhase extends BasePhase {
     async run(context) {
         const config = context.config;
         const { projectRoot, options } = context;
-        // Determine overwrite mode: --upgrade flag OR config setting
-        const shouldOverwrite = options.upgrade || config.skills.overwrite;
+        // Auto-upgrade if version differs (v3.5.3+)
+        const isVersionUpgrade = this.detectVersionUpgrade(context);
+        // Determine overwrite mode: --upgrade flag, config setting, OR auto-mode with version change
+        const shouldOverwrite = options.upgrade || config.skills.overwrite ||
+            (options.autoMode && isVersionUpgrade);
         let skillsInstalled = 0;
         let agentsInstalled = 0;
         let n8nAgents = 0;
@@ -27,6 +32,9 @@ export class AssetsPhase extends BasePhase {
         if (options.upgrade) {
             context.services.log(`  Upgrade mode: overwriting existing files`);
         }
+        else if (options.autoMode && isVersionUpgrade) {
+            context.services.log(`  Version upgrade detected: updating skills and agents`);
+        }
         // Install skills
         if (config.skills.install) {
             const skillsInstaller = createSkillsInstaller({
@@ -82,6 +90,27 @@ export class AssetsPhase extends BasePhase {
             n8nSkills,
         };
     }
+    /**
+     * Detect if this is a version upgrade by comparing existing config version
+     * with the new version being installed
+     */
+    detectVersionUpgrade(context) {
+        const configPath = join(context.projectRoot, '.agentic-qe', 'config.yaml');
+        if (!existsSync(configPath)) {
+            return false;
+        }
+        try {
+            const content = readFileSync(configPath, 'utf-8');
+            const versionMatch = content.match(/version:\s*"?([^"\n]+)"?/);
+            const existingVersion = versionMatch?.[1];
+            const newVersion = context.config.version;
+            // If versions differ, this is an upgrade
+            return existingVersion !== undefined && existingVersion !== newVersion;
+        }
+        catch {
+            return false;
+        }
+    }
 }
 // Instance exported from index.ts
 //# sourceMappingURL=09-assets.js.map

package/v3/dist/init/phases/09-assets.js.map

@@ -1 +1 @@
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package/v3/dist/init/phases/10-workers.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"10-workers.d.ts","sourceRoot":"","sources":["../../../src/init/phases/10-workers.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAMH,OAAO,EACL,SAAS,EACT,KAAK,WAAW,EACjB,MAAM,sBAAsB,CAAC;AAW9B,MAAM,WAAW,aAAa;IAC5B,UAAU,EAAE,MAAM,CAAC;IACnB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,OAAO,CAAC;IACvB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED;;GAEG;AACH,qBAAa,YAAa,SAAQ,SAAS,CAAC,aAAa,CAAC;IACxD,QAAQ,CAAC,IAAI,aAAa;IAC1B,QAAQ,CAAC,WAAW,kCAAkC;IACtD,QAAQ,CAAC,KAAK,OAAO;IACrB,QAAQ,CAAC,QAAQ,SAAS;IAC1B,QAAQ,CAAC,cAAc,6BAA8B;IAE/C,SAAS,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,OAAO,CAAC;cAKvC,GAAG,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,aAAa,CAAC;IAmOjE;;OAEG;YACW,WAAW;IAmHzB;;;;;;;;OAQG;YACW,cAAc;CAyB7B"}

package/v3/dist/init/phases/10-workers.js

@@ -208,12 +208,15 @@ fi
                     context.services.log(`  MCP daemon started (PID: ${daemonPid})`);
                 }
                 else if (daemonError) {
-                    context.services.log(`  MCP daemon failed: ${daemonError}`);
+                    // Non-blocking: MCP will be started by Claude Code via .mcp.json
+                    context.services.log(`  MCP daemon: skipped (will start via Claude Code)`);
+                    context.services.log(`    Note: ${daemonError}`);
                 }
             }
             catch (error) {
+                // Non-blocking error - MCP works fine when Claude Code starts it
                 daemonError = error instanceof Error ? error.message : 'Unknown error';
-                context.services.log(`  MCP daemon error: ${daemonError}`);
+                context.services.log(`  MCP daemon: skipped (Claude Code will start it)`);
             }
         }
         return {

package/v3/dist/init/phases/10-workers.js.map

@@ -1 +1 @@
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package/v3/dist/init/phases/12-verification.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"12-verification.d.ts","sourceRoot":"","sources":["../../../src/init/phases/12-verification.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAOH,OAAO,EACL,SAAS,EACT,KAAK,WAAW,EACjB,MAAM,sBAAsB,CAAC;AAK9B,MAAM,WAAW,kBAAkB;IACjC,QAAQ,EAAE,OAAO,CAAC;IAClB,cAAc,EAAE,OAAO,CAAC;IACxB,WAAW,EAAE,OAAO,CAAC;IACrB,MAAM,EAAE;QACN,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,EAAE,OAAO,CAAC;KACjB,EAAE,CAAC;CACL;AAED;;GAEG;AACH,qBAAa,iBAAkB,SAAQ,SAAS,CAAC,kBAAkB,CAAC;IAClE,QAAQ,CAAC,IAAI,kBAAkB;IAC/B,QAAQ,CAAC,WAAW,yBAAyB;IAC7C,QAAQ,CAAC,KAAK,OAAO;IACrB,QAAQ,CAAC,QAAQ,QAAQ;IACzB,QAAQ,CAAC,cAAc,yCAA0C;cAEjD,GAAG,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,kBAAkB,CAAC;IAuDtE;;OAEG;YACW,gBAAgB;IA8C9B;;;OAGG;YACW,UAAU;IAoBxB;;;OAGG;IACH,OAAO,CAAC,kBAAkB;IAS1B;;;OAGG;IACH,OAAO,CAAC,SAAS;IAoFjB;;OAEG;IACH,OAAO,CAAC,UAAU;IAWlB;;;OAGG;IACH,OAAO,CAAC,YAAY;IA2DpB;;OAEG;IACH,OAAO,CAAC,YAAY;CAwErB"}
+{"version":3,"file":"12-verification.d.ts","sourceRoot":"","sources":["../../../src/init/phases/12-verification.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAOH,OAAO,EACL,SAAS,EACT,KAAK,WAAW,EACjB,MAAM,sBAAsB,CAAC;AAK9B,MAAM,WAAW,kBAAkB;IACjC,QAAQ,EAAE,OAAO,CAAC;IAClB,cAAc,EAAE,OAAO,CAAC;IACxB,WAAW,EAAE,OAAO,CAAC;IACrB,MAAM,EAAE;QACN,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,EAAE,OAAO,CAAC;KACjB,EAAE,CAAC;CACL;AAED;;GAEG;AACH,qBAAa,iBAAkB,SAAQ,SAAS,CAAC,kBAAkB,CAAC;IAClE,QAAQ,CAAC,IAAI,kBAAkB;IAC/B,QAAQ,CAAC,WAAW,yBAAyB;IAC7C,QAAQ,CAAC,KAAK,OAAO;IACrB,QAAQ,CAAC,QAAQ,QAAQ;IACzB,QAAQ,CAAC,cAAc,yCAA0C;cAEjD,GAAG,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,kBAAkB,CAAC;IA4DtE;;OAEG;YACW,gBAAgB;IA8C9B;;;OAGG;YACW,UAAU;IAoBxB;;;OAGG;IACH,OAAO,CAAC,kBAAkB;IAS1B;;;OAGG;IACH,OAAO,CAAC,SAAS;IAoFjB;;OAEG;IACH,OAAO,CAAC,UAAU;IAWlB;;;OAGG;IACH,OAAO,CAAC,YAAY;IA2DpB;;OAEG;IACH,OAAO,CAAC,YAAY;CAwErB"}

package/v3/dist/init/phases/12-verification.js

@@ -49,14 +49,19 @@ export class VerificationPhase extends BasePhase {
             name: 'Version marker',
             passed: versionWritten,
         });
-        // All critical checks must pass
+        // Critical checks must pass; version marker is informational only
+        // (may fail due to better-sqlite3 loading issues but init still succeeds)
         const criticalChecks = ['Database exists', '.agentic-qe directory', 'Config saved'];
         const allCriticalPassed = checks
             .filter(c => criticalChecks.includes(c.name))
             .every(c => c.passed);
         context.services.log('  Verification checks:');
         for (const check of checks) {
-            context.services.log(`    ${check.passed ? '✓' : '✗'} ${check.name}`);
+            const isCritical = criticalChecks.includes(check.name);
+            // Use different icons: ✓ for passed, ✗ for critical failure, ⚠ for optional failure
+            const icon = check.passed ? '✓' : (isCritical ? '✗' : '⚠');
+            const suffix = !isCritical && !check.passed ? ' (optional)' : '';
+            context.services.log(`    ${icon} ${check.name}${suffix}`);
         }
         return {
             verified: allCriticalPassed,

package/v3/dist/init/phases/12-verification.js.map

@@ -1 +1 @@
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package/v3/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@agentic-qe/v3",
-  "version": "3.5.2",
+  "version": "3.5.3",
   "description": "Agentic QE v3 - Domain-Driven Design Architecture with 12 Bounded Contexts, O(log n) coverage analysis, ReasoningBank learning, 51 specialized QE agents",
   "type": "module",
   "main": "./dist/index.js",