agentic-qe 3.6.1 → 3.6.3

package/v3/dist/cli/bundle.js

@@ -223,6 +223,9 @@ var init_memory_backend = __esm({
       cleanupInterval;
       async initialize() {
         this.cleanupInterval = setInterval(() => this.cleanup(), MEMORY_CONSTANTS.CLEANUP_INTERVAL_MS);
+        if (this.cleanupInterval.unref) {
+          this.cleanupInterval.unref();
+        }
       }
       async dispose() {
         if (this.cleanupInterval) {
@@ -11898,6 +11901,9 @@ var HybridMemoryBackend = class {
       () => this.cleanup(),
       this.config.cleanupInterval
     );
+    if (this.cleanupInterval.unref) {
+      this.cleanupInterval.unref();
+    }
     this.initialized = true;
     console.log(`[HybridBackend] Initialized with unified memory: ${this.unifiedMemory.getDbPath()}`);
   }
@@ -63815,7 +63821,7 @@ function checkTestRunners(projectPath) {
 function countVitestTests(projectPath, config) {
   try {
     const output = execSync5(
-      "npx vitest list --reporter=json 2>/dev/null",
+      "npx vitest list --reporter=json",
       {
         cwd: projectPath,
         encoding: "utf-8",
@@ -63875,7 +63881,7 @@ function countTestsRecursive(tests) {
 function countJestTests(projectPath, config) {
   try {
     const output = execSync5(
-      "npx jest --listTests 2>/dev/null",
+      "npx jest --listTests",
       {
         cwd: projectPath,
         encoding: "utf-8",
@@ -63901,7 +63907,7 @@ function countJestTests(projectPath, config) {
 function countCargoTests(projectPath, config) {
   try {
     const output = execSync5(
-      'cargo test --list 2>/dev/null || echo ""',
+      "cargo test --list",
       {
         cwd: projectPath,
         encoding: "utf-8",
@@ -63935,7 +63941,7 @@ function countCargoTests(projectPath, config) {
 function countPytestTests(projectPath, config) {
   try {
     const output = execSync5(
-      'pytest --collect-only -q 2>/dev/null || echo ""',
+      "pytest --collect-only -q",
       {
         cwd: projectPath,
         encoding: "utf-8",
@@ -63976,7 +63982,7 @@ function countPytestTests(projectPath, config) {
 function countGoTests(projectPath, config) {
   try {
     const output = execSync5(
-      'go test -list ".*" ./... 2>/dev/null || echo ""',
+      'go test -list ".*" ./...',
       {
         cwd: projectPath,
         encoding: "utf-8",
@@ -111993,7 +111999,7 @@ var ALL_DOMAINS2 = [
   "enterprise-integration"
 ];
 function getAQEVersion() {
-  return true ? "3.6.1" : "3.0.0";
+  return true ? "3.6.3" : "3.0.0";
 }
 function createDefaultConfig(projectName, projectRoot) {
   return {
@@ -113620,10 +113626,12 @@ var AgentsInstaller = class {
   }
   /**
    * Copy helpers directory (agent-specific reference files, templates, scripts)
+   * Installed to .claude/helpers/v3/ (NOT .claude/agents/v3/helpers/) to avoid
+   * claude doctor parsing .md helper files as agent definitions (Issue #243).
    */
-  async copyHelpersDirectory(targetAgentsDir) {
+  async copyHelpersDirectory(_targetAgentsDir) {
     const sourceHelpersDir = join18(this.sourceAgentsDir, "helpers");
-    const targetHelpersDir = join18(targetAgentsDir, "helpers");
+    const targetHelpersDir = join18(this.projectRoot, ".claude", "helpers", "v3");
     if (existsSync16(sourceHelpersDir)) {
       this.copyDirectoryRecursive(sourceHelpersDir, targetHelpersDir);
     }
@@ -113716,9 +113724,11 @@ var AgentsInstaller = class {
     return domainMap[key];
   }
   /**
-   * Create an agents index file for easy reference
+   * Create an agents index file for easy reference.
+   * Written to .claude/docs/ instead of .claude/agents/v3/ to avoid
+   * claude doctor parsing it as an agent definition (Issue #243).
    */
-  async createAgentsIndex(agentsDir, installed) {
+  async createAgentsIndex(_agentsDir, installed) {
     const qeAgents = installed.filter((a37) => a37.type === "v3-qe");
     const subagents = installed.filter((a37) => a37.type === "v3-subagent");
     const byDomain = /* @__PURE__ */ new Map();
@@ -113773,7 +113783,11 @@ ${subagents.map((a37) => `- **${a37.name}**${a37.description ? `: ${a37.descript
 
 *Generated by AQE v3 init on ${(/* @__PURE__ */ new Date()).toISOString()}*
 `;
-    writeFileSync3(join18(agentsDir, "README.md"), indexContent, "utf-8");
+    const docsDir = join18(this.projectRoot, ".claude", "docs");
+    if (!existsSync16(docsDir)) {
+      mkdirSync6(docsDir, { recursive: true });
+    }
+    writeFileSync3(join18(docsDir, "v3-agents-index.md"), indexContent, "utf-8");
   }
 };
 function createAgentsInstaller(options) {
@@ -115033,7 +115047,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_file_path" ] && aqe hooks pre-edit --file "$TOOL_INPUT_file_path" 2>/dev/null || true',
+              command: 'aqe hooks pre-edit --file "$TOOL_INPUT_file_path"',
               timeout: 5e3,
               continueOnError: true
             }
@@ -115044,7 +115058,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_command" ] && aqe hooks pre-command --command "$TOOL_INPUT_command" 2>/dev/null || true',
+              command: 'aqe hooks pre-command --command "$TOOL_INPUT_command"',
               timeout: 5e3,
               continueOnError: true
             }
@@ -115055,7 +115069,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_prompt" ] && aqe hooks pre-task --task-id "task-$(date +%s)" --description "$TOOL_INPUT_prompt" 2>/dev/null || true',
+              command: 'aqe hooks pre-task --description "$TOOL_INPUT_prompt"',
               timeout: 5e3,
               continueOnError: true
             }
@@ -115069,7 +115083,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_file_path" ] && aqe hooks post-edit --file "$TOOL_INPUT_file_path" --success "${TOOL_SUCCESS:-true}" 2>/dev/null || true',
+              command: 'aqe hooks post-edit --file "$TOOL_INPUT_file_path" --success "$TOOL_SUCCESS"',
               timeout: 5e3,
               continueOnError: true
             }
@@ -115080,7 +115094,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_command" ] && aqe hooks post-command --command "$TOOL_INPUT_command" --success "${TOOL_SUCCESS:-true}" 2>/dev/null || true',
+              command: 'aqe hooks post-command --command "$TOOL_INPUT_command" --success "$TOOL_SUCCESS"',
               timeout: 5e3,
               continueOnError: true
             }
@@ -115091,7 +115105,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_RESULT_agent_id" ] && aqe hooks post-task --task-id "$TOOL_RESULT_agent_id" --success "${TOOL_SUCCESS:-true}" 2>/dev/null || true',
+              command: 'aqe hooks post-task --task-id "$TOOL_RESULT_agent_id" --success "$TOOL_SUCCESS"',
               timeout: 5e3,
               continueOnError: true
             }
@@ -115104,7 +115118,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: '[ -n "$PROMPT" ] && aqe hooks route --task "$PROMPT" 2>/dev/null || true',
+              command: 'aqe hooks route --task "$PROMPT"',
               timeout: 5e3,
               continueOnError: true
             }
@@ -115117,7 +115131,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: '[ -n "$SESSION_ID" ] && aqe hooks session-start --session-id "$SESSION_ID" 2>/dev/null || true',
+              command: 'aqe hooks session-start --session-id "$SESSION_ID"',
               timeout: 1e4,
               continueOnError: true
             }
@@ -115129,7 +115143,7 @@ Ensure the directory is writable and has sufficient disk space.`
           hooks: [
             {
               type: "command",
-              command: "aqe hooks session-end --save-state 2>/dev/null || true",
+              command: "aqe hooks session-end --save-state",
               timeout: 5e3,
               continueOnError: true
             }
@@ -115584,31 +115598,15 @@ aqe init --auto
       };
       writeFileSync5(workerConfigPath, JSON.stringify(workerConfig, null, 2), "utf-8");
     }
-    const daemonScriptPath = join20(workersDir, "start-daemon.sh");
-    const daemonScript = `#!/bin/bash
-# AQE v3 Worker Daemon Startup Script
-# Generated by aqe init
+    const daemonScriptPath = join20(workersDir, "start-daemon.cjs");
+    const daemonScript = `#!/usr/bin/env node
+// AQE v3 Worker Daemon Startup Script (cross-platform)
+// Generated by aqe init
 
-PROJECT_ROOT="${this.projectRoot}"
-WORKERS_DIR="$PROJECT_ROOT/.agentic-qe/workers"
-PID_FILE="$WORKERS_DIR/daemon.pid"
-
-# Check if already running
-if [ -f "$PID_FILE" ]; then
-  PID=$(cat "$PID_FILE")
-  if kill -0 "$PID" 2>/dev/null; then
-    echo "Daemon already running (PID: $PID)"
-    exit 0
-  fi
-fi
-
-# Start daemon (AQE v3 native - no claude-flow dependency)
-# TODO: Implement aqe daemon command for background workers
-# For now, hooks work via CLI without daemon
-echo "AQE v3 hooks work via CLI commands (no daemon required)"
-echo "Use: npx aqe hooks session-start"
+console.log("AQE v3 hooks work via CLI commands (no daemon required)");
+console.log("Use: npx aqe hooks session-start");
 `;
-    writeFileSync5(daemonScriptPath, daemonScript, { mode: 493 });
+    writeFileSync5(daemonScriptPath, daemonScript);
     return config.workers.enabled.length;
   }
   /**
@@ -116424,7 +116422,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_file_path" ] && npx agentic-qe hooks pre-edit --file "$TOOL_INPUT_file_path" --json 2>/dev/null || true',
+              command: 'npx agentic-qe hooks pre-edit --file "$TOOL_INPUT_file_path" --json',
               timeout: 5e3,
               continueOnError: true
             }
@@ -116435,7 +116433,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_command" ] && npx agentic-qe hooks pre-command --command "$TOOL_INPUT_command" --json 2>/dev/null || true',
+              command: 'npx agentic-qe hooks pre-command --command "$TOOL_INPUT_command" --json',
               timeout: 5e3,
               continueOnError: true
             }
@@ -116446,7 +116444,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_prompt" ] && npx agentic-qe hooks pre-task --task-id "task-$(date +%s)" --description "$TOOL_INPUT_prompt" --json 2>/dev/null || true',
+              command: 'npx agentic-qe hooks pre-task --description "$TOOL_INPUT_prompt" --json',
               timeout: 5e3,
               continueOnError: true
             }
@@ -116459,7 +116457,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_file_path" ] && npx agentic-qe hooks post-edit --file "$TOOL_INPUT_file_path" --success "${TOOL_SUCCESS:-true}" --json 2>/dev/null || true',
+              command: 'npx agentic-qe hooks post-edit --file "$TOOL_INPUT_file_path" --success "$TOOL_SUCCESS" --json',
               timeout: 5e3,
               continueOnError: true
             }
@@ -116470,7 +116468,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_INPUT_command" ] && npx agentic-qe hooks post-command --command "$TOOL_INPUT_command" --success "${TOOL_SUCCESS:-true}" --json 2>/dev/null || true',
+              command: 'npx agentic-qe hooks post-command --command "$TOOL_INPUT_command" --success "$TOOL_SUCCESS" --json',
               timeout: 5e3,
               continueOnError: true
             }
@@ -116481,7 +116479,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: '[ -n "$TOOL_RESULT_agent_id" ] && npx agentic-qe hooks post-task --task-id "$TOOL_RESULT_agent_id" --success "${TOOL_SUCCESS:-true}" --json 2>/dev/null || true',
+              command: 'npx agentic-qe hooks post-task --task-id "$TOOL_RESULT_agent_id" --success "$TOOL_SUCCESS" --json',
               timeout: 5e3,
               continueOnError: true
             }
@@ -116493,7 +116491,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: '[ -n "$PROMPT" ] && npx agentic-qe hooks route --task "$PROMPT" --json 2>/dev/null || true',
+              command: 'npx agentic-qe hooks route --task "$PROMPT" --json',
               timeout: 5e3,
               continueOnError: true
             }
@@ -116505,7 +116503,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: '[ -n "$SESSION_ID" ] && npx agentic-qe hooks session-start --session-id "$SESSION_ID" --json 2>/dev/null || true',
+              command: 'npx agentic-qe hooks session-start --session-id "$SESSION_ID" --json',
               timeout: 1e4,
               continueOnError: true
             }
@@ -116517,7 +116515,7 @@ var HooksPhase = class extends BasePhase {
           hooks: [
             {
               type: "command",
-              command: "npx agentic-qe hooks session-end --save-state --json 2>/dev/null || true",
+              command: "npx agentic-qe hooks session-end --save-state --json",
               timeout: 5e3,
               continueOnError: true
             }
@@ -116794,102 +116792,91 @@ var WorkersPhase = class extends BasePhase {
       };
       writeFileSync9(workerConfigPath, JSON.stringify(workerConfig, null, 2), "utf-8");
     }
-    const daemonScriptPath = join28(workersDir, "start-daemon.sh");
-    const daemonScript = `#!/bin/bash
-# AQE v3 Worker Daemon Startup Script
-# Generated by aqe init
-# Starts the MCP server with background workers enabled
-
-# Get directory where this script is located
-SCRIPT_DIR="$(cd "$(dirname "\${BASH_SOURCE[0]}")" && pwd)"
-# Navigate up from .agentic-qe/workers to project root
-PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
-WORKERS_DIR="$PROJECT_ROOT/.agentic-qe/workers"
-PID_FILE="$WORKERS_DIR/daemon.pid"
-LOG_FILE="$WORKERS_DIR/daemon.log"
-
-# Check if already running
-if [ -f "$PID_FILE" ]; then
-  PID=$(cat "$PID_FILE")
-  if kill -0 "$PID" 2>/dev/null; then
-    echo "Daemon already running (PID: $PID)"
-    exit 0
-  fi
-fi
-
-echo "[$(date)] Starting AQE v3 Worker Daemon..." >> "$LOG_FILE"
-
-# Set environment for learning and workers
-export AQE_PROJECT_ROOT="$PROJECT_ROOT"
-export AQE_LEARNING_ENABLED=true
-export AQE_WORKERS_ENABLED=true
-export AQE_HTTP_PORT=0
-
-# Find the best way to run aqe-mcp
-MCP_CMD=""
-if [ -f "$PROJECT_ROOT/node_modules/.bin/aqe-mcp" ]; then
-  MCP_CMD="$PROJECT_ROOT/node_modules/.bin/aqe-mcp"
-elif [ -f "$PROJECT_ROOT/node_modules/agentic-qe/v3/dist/mcp/bundle.js" ]; then
-  MCP_CMD="node $PROJECT_ROOT/node_modules/agentic-qe/v3/dist/mcp/bundle.js"
-elif [ -f "$PROJECT_ROOT/node_modules/.bin/aqe" ]; then
-  # Use aqe CLI with mcp subcommand
-  MCP_CMD="$PROJECT_ROOT/node_modules/.bin/aqe mcp"
-elif command -v aqe-mcp &> /dev/null; then
-  MCP_CMD="aqe-mcp"
-elif command -v aqe &> /dev/null; then
-  # Use global aqe CLI with mcp subcommand
-  MCP_CMD="aqe mcp"
-else
-  # Fallback to npx - aqe CLI has mcp subcommand
-  MCP_CMD="npx --yes agentic-qe mcp"
-fi
-
-echo "[$(date)] Using MCP command: $MCP_CMD" >> "$LOG_FILE"
-
-# Start the MCP server with workers
-cd "$PROJECT_ROOT"
-nohup $MCP_CMD >> "$LOG_FILE" 2>&1 &
-DAEMON_PID=$!
-
-# Save PID
-echo $DAEMON_PID > "$PID_FILE"
-echo "[$(date)] Daemon started with PID: $DAEMON_PID" >> "$LOG_FILE"
-
-echo "AQE v3 Worker Daemon started (PID: $DAEMON_PID)"
-echo "Log file: $LOG_FILE"
-echo ""
-echo "To stop: kill $DAEMON_PID"
-echo "To view logs: tail -f $LOG_FILE"
-`;
-    writeFileSync9(daemonScriptPath, daemonScript, { mode: 493 });
-    const stopScriptPath = join28(workersDir, "stop-daemon.sh");
-    const stopScript = `#!/bin/bash
-# AQE v3 Worker Daemon Stop Script
-# Generated by aqe init
+    const daemonScriptPath = join28(workersDir, "start-daemon.cjs");
+    const daemonScript = `#!/usr/bin/env node
+// AQE v3 Worker Daemon Startup Script (cross-platform)
+// Generated by aqe init
+// Starts the MCP server with background workers enabled
+
+const { existsSync, readFileSync, writeFileSync, appendFileSync } = require('fs');
+const { join } = require('path');
+const { spawn } = require('child_process');
 
-# Get directory where this script is located
-SCRIPT_DIR="$(cd "$(dirname "\${BASH_SOURCE[0]}")" && pwd)"
-# Navigate up from .agentic-qe/workers to project root
-PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
-WORKERS_DIR="$PROJECT_ROOT/.agentic-qe/workers"
-PID_FILE="$WORKERS_DIR/daemon.pid"
-
-if [ -f "$PID_FILE" ]; then
-  PID=$(cat "$PID_FILE")
-  if kill -0 "$PID" 2>/dev/null; then
-    echo "Stopping daemon (PID: $PID)..."
-    kill "$PID"
-    rm -f "$PID_FILE"
-    echo "Daemon stopped"
-  else
-    echo "Daemon not running (stale PID file)"
-    rm -f "$PID_FILE"
-  fi
-else
-  echo "No PID file found - daemon may not be running"
-fi
+const projectRoot = join(__dirname, '..', '..');
+const workersDir = join(projectRoot, '.agentic-qe', 'workers');
+const pidFile = join(workersDir, 'daemon.pid');
+const logFile = join(workersDir, 'daemon.log');
+
+// Check if already running
+if (existsSync(pidFile)) {
+  const pid = parseInt(readFileSync(pidFile, 'utf-8').trim(), 10);
+  try { process.kill(pid, 0); console.log('Daemon already running (PID: ' + pid + ')'); process.exit(0); } catch {}
+}
+
+const ts = new Date().toISOString();
+appendFileSync(logFile, '[' + ts + '] Starting AQE v3 Worker Daemon...\\n');
+
+// Find the best way to run aqe-mcp
+const candidates = [
+  join(projectRoot, 'node_modules', '.bin', 'aqe-mcp'),
+  join(projectRoot, 'node_modules', 'agentic-qe', 'v3', 'dist', 'mcp', 'bundle.js'),
+];
+
+let mcpCmd, mcpArgs;
+const binCandidate = candidates.find(c => existsSync(c));
+
+if (binCandidate && binCandidate.endsWith('bundle.js')) {
+  mcpCmd = process.execPath;
+  mcpArgs = [binCandidate];
+} else if (binCandidate) {
+  mcpCmd = binCandidate;
+  mcpArgs = [];
+} else {
+  mcpCmd = process.platform === 'win32' ? 'npx.cmd' : 'npx';
+  mcpArgs = ['--yes', 'agentic-qe', 'mcp'];
+}
+
+appendFileSync(logFile, '[' + ts + '] Using: ' + mcpCmd + ' ' + mcpArgs.join(' ') + '\\n');
+
+const env = { ...process.env, AQE_PROJECT_ROOT: projectRoot, AQE_LEARNING_ENABLED: 'true', AQE_WORKERS_ENABLED: 'true', AQE_HTTP_PORT: '0' };
+const child = spawn(mcpCmd, mcpArgs, { cwd: projectRoot, env, detached: true, stdio: ['ignore', 'pipe', 'pipe'] });
+child.stdout.on('data', d => appendFileSync(logFile, d));
+child.stderr.on('data', d => appendFileSync(logFile, d));
+child.unref();
+
+writeFileSync(pidFile, String(child.pid));
+appendFileSync(logFile, '[' + ts + '] Daemon started with PID: ' + child.pid + '\\n');
+console.log('AQE v3 Worker Daemon started (PID: ' + child.pid + ')');
+console.log('Log file: ' + logFile);
+console.log('To stop: node ' + join(workersDir, 'stop-daemon.cjs'));
 `;
-    writeFileSync9(stopScriptPath, stopScript, { mode: 493 });
+    writeFileSync9(daemonScriptPath, daemonScript);
+    const stopScriptPath = join28(workersDir, "stop-daemon.cjs");
+    const stopScript = `#!/usr/bin/env node
+// AQE v3 Worker Daemon Stop Script (cross-platform)
+// Generated by aqe init
+
+const { existsSync, readFileSync, unlinkSync } = require('fs');
+const { join } = require('path');
+
+const workersDir = join(__dirname);
+const pidFile = join(workersDir, 'daemon.pid');
+
+if (!existsSync(pidFile)) { console.log('No PID file found - daemon may not be running'); process.exit(0); }
+
+const pid = parseInt(readFileSync(pidFile, 'utf-8').trim(), 10);
+try {
+  process.kill(pid, 0); // Check if alive
+  console.log('Stopping daemon (PID: ' + pid + ')...');
+  process.kill(pid, 'SIGTERM');
+  try { unlinkSync(pidFile); } catch {}
+  console.log('Daemon stopped');
+} catch {
+  console.log('Daemon not running (stale PID file)');
+  try { unlinkSync(pidFile); } catch {}
+}
+`;
+    writeFileSync9(stopScriptPath, stopScript);
     context2.services.log(`  Workers dir: ${workersDir}`);
     context2.services.log(`  Workers: ${config.workers.enabled.join(", ")}`);
     let daemonStarted = false;
@@ -117355,6 +117342,17 @@ var VerificationPhase = class extends BasePhase {
           section[currentSubSection].push(arrayMatch[1]);
         }
       }
+      const arrayFields = [
+        ["domains", "enabled"],
+        ["domains", "disabled"],
+        ["workers", "enabled"]
+      ];
+      for (const [section, field] of arrayFields) {
+        const sec = result[section];
+        if (sec && field in sec && !Array.isArray(sec[field])) {
+          sec[field] = [];
+        }
+      }
       return result;
     } catch {
       return null;
@@ -117384,7 +117382,9 @@ var VerificationPhase = class extends BasePhase {
       for (const domain of newDomains) {
         existingDomains.add(domain);
       }
-      const disabledDomains = new Set(existing.domains?.disabled || []);
+      const disabledDomains = new Set(
+        Array.isArray(existing.domains?.disabled) ? existing.domains.disabled : []
+      );
       newConfig.domains.enabled = Array.from(existingDomains).filter((d74) => !disabledDomains.has(d74));
     }
     if (existing.domains?.disabled && Array.isArray(existing.domains.disabled)) {
@@ -117906,7 +117906,7 @@ async function detectClaudeFlow(projectRoot, debug) {
     }
   }
   try {
-    const result = execSync6("npx @claude-flow/cli@latest --version 2>/dev/null", {
+    const result = execSync6("npx @claude-flow/cli@latest --version", {
       encoding: "utf-8",
       timeout: 1e4,
       cwd: projectRoot
@@ -117947,7 +117947,7 @@ async function detectFeatures(projectRoot) {
   ];
   for (const check of featureChecks) {
     try {
-      execSync6(`npx @claude-flow/cli@latest ${check.command} 2>/dev/null`, {
+      execSync6(`npx @claude-flow/cli@latest ${check.command}`, {
         encoding: "utf-8",
         timeout: 5e3,
         cwd: projectRoot
@@ -118023,7 +118023,7 @@ function updateMCPConfig(projectRoot) {
 async function runPretrainAnalysis(projectRoot, debug) {
   try {
     if (debug) console.log("[ClaudeFlow] Running pretrain analysis...");
-    execSync6("npx @claude-flow/cli@latest hooks pretrain --depth medium 2>/dev/null", {
+    execSync6("npx @claude-flow/cli@latest hooks pretrain --depth medium", {
       encoding: "utf-8",
       timeout: 12e4,
       // 2 minutes
@@ -123160,24 +123160,25 @@ function detectShell() {
       detected: true
     };
   }
+  const homeDir = process.env.HOME || process.env.USERPROFILE || "";
   if (shell.includes("bash")) {
     return {
       name: "bash",
-      configFile: `${process.env.HOME}/.bashrc`,
+      configFile: `${homeDir}/.bashrc`,
       detected: true
     };
   }
   if (shell.includes("zsh")) {
     return {
       name: "zsh",
-      configFile: `${process.env.HOME}/.zshrc`,
+      configFile: `${homeDir}/.zshrc`,
       detected: true
     };
   }
   if (shell.includes("fish")) {
     return {
       name: "fish",
-      configFile: `${process.env.HOME}/.config/fish/completions/aqe.fish`,
+      configFile: `${homeDir}/.config/fish/completions/aqe.fish`,
       detected: true
     };
   }
@@ -123270,7 +123271,8 @@ Installing completions for ${shellInfo.name}...
 `));
     const script = generateCompletion(shellInfo.name);
     if (shellInfo.name === "fish") {
-      const fishCompletionsDir = `${process.env.HOME}/.config/fish/completions`;
+      const homeDir = process.env.HOME || process.env.USERPROFILE || "";
+      const fishCompletionsDir = path23.join(homeDir, ".config", "fish", "completions");
       try {
         fs21.mkdirSync(fishCompletionsDir, { recursive: true });
         const completionFile = path23.join(fishCompletionsDir, "aqe.fish");
@@ -130544,6 +130546,16 @@ var IAPTunnelManager = class {
       console.log("[TunnelManager] Tunnel already running");
       return this.connection;
     }
+    const alreadyListening = await this.checkPort("localhost", this.config.tunnelPort);
+    if (alreadyListening) {
+      console.log(`[TunnelManager] External tunnel detected on port ${this.config.tunnelPort}, reusing`);
+      this.connection = {
+        host: "localhost",
+        port: this.config.tunnelPort,
+        startedAt: /* @__PURE__ */ new Date()
+      };
+      return this.connection;
+    }
     return new Promise((resolve14, reject) => {
       const args = [
         "compute",
@@ -136543,10 +136555,11 @@ Registered: ${events.length}/${Object.keys(QE_HOOK_EVENTS).length}`)
     try {
       const sessionId = state.sessionId || "unknown";
       let stats = null;
-      try {
-        const { reasoningBank } = await getHooksSystem();
-        stats = await reasoningBank.getStats();
-      } catch {
+      if (state.initialized && state.reasoningBank) {
+        try {
+          stats = await state.reasoningBank.getStats();
+        } catch {
+        }
       }
       if (options.json) {
         printJson({
@@ -138420,7 +138433,7 @@ async function cleanupAndExit(code = 0) {
   process.exit(code);
 }
 var program = new Command18();
-var VERSION = true ? "3.6.1" : "0.0.0-dev";
+var VERSION = true ? "3.6.3" : "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/cli/commands/claude-flow-setup.js

@@ -44,7 +44,7 @@ async function detectClaudeFlow(projectRoot, debug) {
     }
     // Method 2: Check for CLI availability
     try {
-        const result = execSync('npx @claude-flow/cli@latest --version 2>/dev/null', {
+        const result = execSync('npx @claude-flow/cli@latest --version', {
             encoding: 'utf-8',
             timeout: 10000,
             cwd: projectRoot,
@@ -96,7 +96,7 @@ async function detectFeatures(projectRoot) {
     ];
     for (const check of featureChecks) {
         try {
-            execSync(`npx @claude-flow/cli@latest ${check.command} 2>/dev/null`, {
+            execSync(`npx @claude-flow/cli@latest ${check.command}`, {
                 encoding: 'utf-8',
                 timeout: 5000,
                 cwd: projectRoot,
@@ -192,7 +192,7 @@ async function runPretrainAnalysis(projectRoot, debug) {
     try {
         if (debug)
             console.log('[ClaudeFlow] Running pretrain analysis...');
-        execSync('npx @claude-flow/cli@latest hooks pretrain --depth medium 2>/dev/null', {
+        execSync('npx @claude-flow/cli@latest hooks pretrain --depth medium', {
             encoding: 'utf-8',
             timeout: 120000, // 2 minutes
             cwd: projectRoot,