forge-workflow 0.0.6 → 0.0.7

package/lib/commands/setup.js

@@ -0,0 +1,4295 @@
+'use strict';
+
+/**
+ * Setup Command — Extracted from bin/forge.js
+ *
+ * Contains all setup-related functions: interactive setup, agent configuration,
+ * tool installation, external services, dry-run, quick mode, etc.
+ *
+ * @module commands/setup
+ */
+
+const fs = require('node:fs');
+const path = require('node:path');
+const readline = require('node:readline');
+const { execSync, execFileSync } = require('node:child_process');
+
+// Compute packageDir relative to this file (lib/commands/setup.js -> project root)
+const packageDir = path.resolve(__dirname, '..', '..');
+const packageJson = require(path.join(packageDir, 'package.json'));
+const VERSION = packageJson.version;
+
+// Load PluginManager for discoverable agent architecture
+const PluginManager = require('../plugin-manager');
+const { scaffoldGithubBeadsSync } = require('../setup');
+const { copyEssentialDocs } = require('../docs-copy');
+const { secureExecFileSync } = require('../shell-utils');
+const { askYesNo: _askYesNoBase } = require('../ui-utils');
+
+// Load enhanced onboarding modules
+const contextMerge = require(path.join(packageDir, 'lib', 'context-merge'));
+const projectDiscovery = require(path.join(packageDir, 'lib', 'project-discovery'));
+
+// Load lib modules for symlink, beads, and PAT setup
+const { createSymlinkOrCopy: libCreateSymlinkOrCopy } = require(path.join(packageDir, 'lib', 'symlink-utils'));
+const beadsSetupLib = require(path.join(packageDir, 'lib', 'beads-setup'));
+const { beadsHealthCheck } = require(path.join(packageDir, 'lib', 'beads-health-check'));
+const { setupPAT } = require(path.join(packageDir, 'lib', 'pat-setup'));
+const { detectDefaultBranch, detectBeadsVersion, templateWorkflows, scaffoldBeadsSync } = require(path.join(packageDir, 'lib', 'beads-sync-scaffold'));
+
+// Load incremental setup modules
+const { detectEnvironment } = require('../detect-agent');
+const { fileMatchesContent } = require('../file-hash');
+const { SetupActionLog } = require('../setup-action-log');
+const { ActionCollector } = require('../setup-utils');
+const { renderSetupSummary } = require('../setup-summary-renderer');
+const { smartMergeAgentsMd } = require('../smart-merge');
+const { checkLefthookStatus } = require('../lefthook-check');
+const { resolveShellRuntime } = require('../runtime-health');
+const { listCodexSkillEntries } = require('../codex-skills');
+const {
+  generateCopilotConfig,
+  generateCursorConfig,
+  generateKiloConfig,
+  generateOpenCodeConfig,
+} = require('../agents-config');
+const fileUtils = require('../file-utils');
+const detectionUtils = require('../detection-utils');
+const { detectHusky, migrateHusky } = require('../husky-migration');
+
+// --- Module-level state (deferred from ForgeContext migration) ---
+// Follow-up tracked in forge-vi7v: migrate setup state to a ForgeContext instance passed via handler args.
+// Setup's ~100 functions reference these globals extensively; converting all
+// call sites is a separate task to avoid scope creep in the extraction PR.
+let projectRoot = process.env.INIT_CWD || process.cwd();
+let FORCE_MODE = false;
+let VERBOSE_MODE = false;
+let NON_INTERACTIVE = false;
+let SYMLINK_ONLY = false;
+let SYNC_ENABLED = false;
+let actionLog = new SetupActionLog();
+let PKG_MANAGER = 'npm';
+
+/**
+ * Load agent definitions from plugin architecture
+ * (Duplicated from bin/forge.js to keep setup self-contained)
+ */
+function loadAgentsFromPlugins() {
+  const pluginManager = new PluginManager();
+  const agents = {};
+  pluginManager.getAllPlugins().forEach((plugin, id) => {
+    agents[id] = {
+      name: plugin.name,
+      description: plugin.description || '',
+      dirs: Object.values(plugin.directories || {}),
+      hasCommands: plugin.capabilities?.commands || plugin.setup?.copyCommands || false,
+      hasSkill: plugin.capabilities?.skills || plugin.setup?.createSkill || false,
+      linkFile: plugin.files?.rootConfig || '',
+      customSetup: plugin.setup?.customSetup || '',
+      supportStatus: plugin.support?.status || 'supported',
+      needsConversion: plugin.setup?.needsConversion || false,
+      copyCommands: plugin.setup?.copyCommands || false,
+      promptFormat: plugin.setup?.promptFormat || false
+    };
+  });
+  return agents;
+}
+
+const AGENTS = loadAgentsFromPlugins();
+Object.freeze(AGENTS);
+Object.values(AGENTS).forEach(agent => Object.freeze(agent));
+
+/**
+ * Safe exec helper (duplicated from bin/forge.js)
+ */
+function safeExec(cmd, opts = {}) {
+  try {
+    return execSync(cmd, { stdio: 'pipe', ...opts }).toString().trim();
+  } catch (_e) { // NOSONAR — intentional: safeExec returns empty string on any failure
+    return '';
+  }
+}
+
+/**
+ * Detect package manager
+ */
+function detectPackageManager() {
+  if (fs.existsSync(path.join(projectRoot, 'bun.lockb')) || fs.existsSync(path.join(projectRoot, 'bun.lock'))) return 'bun';
+  if (fs.existsSync(path.join(projectRoot, 'pnpm-lock.yaml'))) return 'pnpm';
+  if (fs.existsSync(path.join(projectRoot, 'yarn.lock'))) return 'yarn';
+  return 'npm';
+}
+
+/**
+ * Reads workflow command names from commands/*.md in the package directory.
+ * Falls back to .claude/commands/ if commands/ does not exist (backwards compat).
+ * @returns {string[]} Command names (filenames without .md extension)
+ */
+function getWorkflowCommands() {
+  const canonicalDir = path.join(packageDir, 'commands');
+  const commandsDir = fs.existsSync(canonicalDir)
+    ? canonicalDir
+    : path.join(packageDir, '.claude', 'commands');
+  try {
+    return fs.readdirSync(commandsDir)
+      .filter(f => f.endsWith('.md'))
+      .map(f => f.replace(/\.md$/, ''));
+  } catch (err) {
+    if (err.code === 'ENOENT') {
+      console.warn(`Warning: commands directory not found at ${commandsDir}`);
+    } else {
+      console.warn(`Warning: failed to read commands — ${err.code}: ${err.message}`);
+    }
+    return [];
+  }
+}
+
+const WORKFLOW_RUNTIME_ASSETS = Object.freeze([
+  'scripts/beads-context.sh',
+  'scripts/conflict-detect.sh',
+  'scripts/dep-guard-analyze.js',
+  'scripts/dep-guard.sh',
+  'scripts/file-index.sh',
+  'scripts/pr-coordinator.sh',
+  'scripts/smart-status.sh',
+  'scripts/sync-utils.sh',
+  'scripts/validate.sh',
+  'scripts/lib/jsonl-lock.sh',
+  'scripts/lib/sanitize.sh',
+  'scripts/forge-team/index.sh',
+  'scripts/forge-team/lib/agent-prompt.sh',
+  'scripts/forge-team/lib/claim.sh',
+  'scripts/forge-team/lib/dashboard.sh',
+  'scripts/forge-team/lib/epic.sh',
+  'scripts/forge-team/lib/hooks.sh',
+  'scripts/forge-team/lib/identity.sh',
+  'scripts/forge-team/lib/sync-github.sh',
+  'scripts/forge-team/lib/verify.sh',
+  'scripts/forge-team/lib/workload.sh',
+  '.claude/scripts/greptile-resolve.sh'
+]);
+
+/**
+ * Validate agent names against known AGENTS.
+ * @param {string} agentList - Comma-separated agent names
+ * @returns {string[]} Valid agent names
+ */
+function validateAgents(agentList) {
+  const requested = agentList.split(',').map(a => a.trim().toLowerCase()).filter(Boolean);
+  const valid = requested.filter(a => AGENTS[a]);
+  const invalid = requested.filter(a => !AGENTS[a]);
+
+  if (invalid.length > 0) {
+    console.log(`  Warning: Unknown agents ignored: ${invalid.join(', ')}`);
+    console.log(`  Available agents: ${Object.keys(AGENTS).join(', ')}`);
+  }
+
+  return valid;
+}
+
+// Prerequisite check function
+function checkPrerequisites(options = {}) {
+  const requireGithubCli = options.requireGithubCli !== false;
+  const requireBeadsCli = options.requireBeadsCli === true;
+  const requireJq = options.requireJq === true;
+  const commandRunner = options.commandRunner || safeExec;
+  const errors = [];
+  const warnings = [];
+
+  console.log('');
+  console.log('Checking prerequisites...');
+  console.log('');
+
+  // Check git
+  const gitVersion = commandRunner('git --version');
+  if (gitVersion) {
+    console.log(`  ✓ ${gitVersion}`);
+  } else {
+    errors.push('git - Install from https://git-scm.com');
+  }
+
+  // Check GitHub CLI
+  const ghVersion = commandRunner('gh --version');
+  if (ghVersion) {
+    const firstLine = ghVersion.split('\n')[0];
+    console.log(`  ✓ ${firstLine}`);
+    // Check if authenticated
+    const authStatus = commandRunner('gh auth status');
+    if (!authStatus) {
+      warnings.push('GitHub CLI not authenticated. Run: gh auth login');
+    }
+  } else {
+    const message = 'gh (GitHub CLI) - Install from https://cli.github.com';
+    if (requireGithubCli) {
+      errors.push(message);
+    } else {
+      warnings.push(`${message} (required later for GitHub-integrated workflow steps)`);
+    }
+  }
+
+  const bdVersion = commandRunner('bd --version');
+  if (bdVersion) {
+    console.log(`  ✓ ${bdVersion.split('\n')[0]}`);
+  } else if (requireBeadsCli) {
+    errors.push('bd (Beads CLI) - Install from https://github.com/steveyegge/beads');
+  }
+
+  // Check Node.js version
+  const nodeVersion = Number.parseInt(process.version.slice(1).split('.')[0]);
+  if (nodeVersion >= 20) {
+    console.log(`  ✓ node ${process.version}`);
+  } else {
+    errors.push(`Node.js 20+ required (current: ${process.version})`);
+  }
+
+  const jqVersion = commandRunner('jq --version');
+  if (jqVersion) {
+    console.log(`  ✓ ${jqVersion.split('\n')[0]}`);
+  } else if (requireJq) {
+    errors.push('jq - Install from https://jqlang.org/download/');
+  }
+
+  // Detect package manager
+  detectPackageManager();
+
+  // Show errors
+  if (errors.length > 0) {
+    console.log('');
+    console.log('❌ Missing required tools:');
+    errors.forEach(err => console.log(`   - ${err}`));
+    console.log('');
+    console.log('Please install missing tools and try again.');
+    process.exit(1);
+  }
+
+  // Show warnings
+  if (warnings.length > 0) {
+    console.log('');
+    console.log('⚠️  Warnings:');
+    warnings.forEach(warn => console.log(`   - ${warn}`));
+  }
+
+  console.log('');
+  console.log(`  Package manager: ${PKG_MANAGER}`);
+
+  return { errors, warnings };
+}
+
+function requiresGithubCliForSetup(selectedAgents, options = {}) {
+  return needsWorkflowRuntimeAssets(selectedAgents) || options.syncEnabled === true;
+}
+
+// Universal SKILL.md content
+const SKILL_CONTENT = `---
+name: forge-workflow
+description: 7-stage TDD-first workflow for feature development. Use when building features, fixing bugs, or shipping PRs.
+category: Development Workflow
+tags: [tdd, workflow, pr, git, testing]
+tools: [Bash, Read, Write, Edit, Grep, Glob]
+---
+
+# Forge Workflow Skill
+
+A TDD-first workflow for AI coding agents. Ship features with confidence.
+
+## When to Use
+
+Automatically invoke this skill when the user wants to:
+- Build a new feature
+- Fix a bug
+- Create a pull request
+- Run the development workflow
+
+## 7 Stages
+
+| Stage | Command | Description |
+|-------|---------|-------------|
+| utility | \`/status\` | Check current context, active work, recent completions |
+| 1 | \`/plan\` | Design intent -> research -> branch + worktree + task list |
+| 2 | \`/dev\` | TDD development (implementer -> spec review -> quality review) |
+| 3 | \`/validate\` | Type check, lint, security, tests - all fresh output |
+| 4 | \`/ship\` | Push branch and create PR with full documentation |
+| 5 | \`/review\` | Address ALL PR feedback (GitHub Actions, Greptile, SonarCloud) |
+| 6 | \`/premerge\` | Update docs, hand off PR to user |
+| 7 | \`/verify\` | Post-merge health check (CI on main, close Beads) |
+
+## Workflow Flow
+
+\`\`\`
+/status -> /plan -> /dev -> /validate -> /ship -> /review -> /premerge -> /verify
+\`\`\`
+
+## Core Principles
+
+- **TDD-First**: Write tests BEFORE implementation (RED-GREEN-REFACTOR)
+- **Research-First**: Understand before building, document decisions
+- **Security Built-In**: OWASP Top 10 analysis for every feature
+- **Documentation Progressive**: Update at each stage, verify at end
+`;
+
+// Helper functions
+
+
+
+// Helper functions
+
+function ensureDir(dir) {
+  return fileUtils.ensureDir(dir, projectRoot);
+}
+
+
+
+function writeFile(filePath, content) {
+  return fileUtils.writeFile(filePath, content, projectRoot);
+}
+
+
+
+function readFile(filePath) {
+  return fileUtils.readFile(filePath);
+}
+
+
+
+function copyFile(src, dest) { // NOSONAR — Extracted as-is from bin/forge.js; complexity reduction deferred
+  try {
+    const destPath = path.resolve(projectRoot, dest);
+    const resolvedProjectRoot = path.resolve(projectRoot);
+
+    // SECURITY: Prevent path traversal
+    if (!destPath.startsWith(resolvedProjectRoot)) {
+      console.error(`  ✗ Security: Copy destination escape blocked: ${dest}`);
+      return false;
+    }
+
+    if (fs.existsSync(src)) {
+      // Content-hash comparison: skip if destination already matches source
+      if (!FORCE_MODE) {
+        const sourceContent = fs.readFileSync(src, 'utf8');
+        if (fileMatchesContent(destPath, sourceContent)) {
+          actionLog.add(dest, 'skipped', 'identical content');
+          return true;
+        }
+      }
+
+      const destDir = path.dirname(destPath);
+      if (!fs.existsSync(destDir)) {
+        fs.mkdirSync(destDir, { recursive: true });
+      }
+      const isNew = !fs.existsSync(destPath);
+      fs.copyFileSync(src, destPath);
+      let action;
+      if (FORCE_MODE) {
+        action = 'force-created';
+      } else {
+        action = isNew ? 'created' : 'updated';
+      }
+      actionLog.add(dest, action);
+      return true;
+    } else {
+      console.warn(`  ⚠ Source file not found: ${src}`);
+    }
+  } catch (err) {
+    console.error(`  ✗ Failed to copy ${src} -> ${dest}: ${err.message}`);
+  }
+  return false;
+}
+
+function needsWorkflowRuntimeAssets(selectedAgents) {
+  return selectedAgents.some((agentKey) => {
+    const agent = AGENTS[agentKey];
+    return Boolean(agent && (agent.hasCommands || agent.needsConversion || agent.copyCommands || agent.promptFormat));
+  });
+}
+
+function getWorkflowRuntimeAssets() {
+  return [...WORKFLOW_RUNTIME_ASSETS];
+}
+
+function resolveWorkflowRuntimeAgents(targetRoot = projectRoot, selectedAgents = null) {
+  if (Array.isArray(selectedAgents)) {
+    return selectedAgents.filter((agentKey) => AGENTS[agentKey]);
+  }
+
+  return resolveConfiguredWorkflowAgents(targetRoot);
+}
+
+function findMissingWorkflowRuntimeAssets(targetRoot = projectRoot, selectedAgents = null) {
+  const agents = resolveWorkflowRuntimeAgents(targetRoot, selectedAgents);
+  if (!needsWorkflowRuntimeAssets(agents)) {
+    return [];
+  }
+
+  return WORKFLOW_RUNTIME_ASSETS.filter((relativePath) => !fs.existsSync(path.join(targetRoot, relativePath)));
+}
+
+function resolveConfiguredWorkflowAgents(targetRoot = projectRoot) {
+  const configuredAgents = detectConfiguredAgents(targetRoot)
+    .map(normalizeDetectedAgent)
+    .filter((agentName) => AGENTS[agentName]);
+
+  return configuredAgents;
+}
+
+function scaffoldWorkflowRuntimeAssets(selectedAgents) {
+  if (!needsWorkflowRuntimeAssets(selectedAgents)) {
+    return [];
+  }
+
+  for (const relativePath of WORKFLOW_RUNTIME_ASSETS) {
+    const sourcePath = path.join(packageDir, relativePath);
+    copyFile(sourcePath, relativePath);
+  }
+
+  return findMissingWorkflowRuntimeAssets(projectRoot, selectedAgents);
+}
+
+function ensureWorkflowRuntimeAssets(selectedAgents) {
+  const missingAssets = scaffoldWorkflowRuntimeAssets(selectedAgents);
+  if (missingAssets.length > 0) {
+    throw new Error(`setup is incomplete: missing workflow runtime assets: ${missingAssets.join(', ')}`);
+  }
+}
+
+function repairWorkflowRuntimeAssets(targetRoot = projectRoot, selectedAgents = null) {
+  const agents = resolveWorkflowRuntimeAgents(targetRoot, selectedAgents);
+
+  const missingBefore = findMissingWorkflowRuntimeAssets(targetRoot, agents);
+  if (missingBefore.length === 0) {
+    return { attempted: false, agents, repaired: [], missing: [] };
+  }
+
+  const previousRoot = projectRoot;
+  projectRoot = targetRoot;
+  try {
+    const missingAfter = scaffoldWorkflowRuntimeAssets(agents);
+    return {
+      attempted: true,
+      agents,
+      repaired: missingBefore.filter((assetPath) => !missingAfter.includes(assetPath)),
+      missing: missingAfter,
+    };
+  } finally {
+    projectRoot = previousRoot;
+  }
+}
+
+async function repairRuntimeReadiness(selectedAgents = null, options = {}) {
+  const targetRoot = options.projectRoot || projectRoot;
+  const agents = selectedAgents && selectedAgents.length > 0
+    ? selectedAgents
+    : resolveConfiguredWorkflowAgents(targetRoot);
+  const previousRoot = projectRoot;
+  const previousInteractive = NON_INTERACTIVE;
+
+  projectRoot = targetRoot;
+  NON_INTERACTIVE = true;
+
+  try {
+    const shellPolicy = ensureWorkflowShellPolicy(agents, options);
+    const runtimeAssets = repairWorkflowRuntimeAssets(targetRoot, agents);
+
+    if (options.installLefthook !== false) {
+      repairDeclaredLefthookDependency(agents);
+    }
+    if (options.migrateHusky !== false) {
+      await handleHuskyMigration();
+    }
+    if (options.installHooks !== false) {
+      installGitHooks();
+    }
+
+    return {
+      agents,
+      shellPolicy,
+      ...runtimeAssets,
+    };
+  } finally {
+    projectRoot = previousRoot;
+    NON_INTERACTIVE = previousInteractive;
+  }
+}
+
+function resolveWorkflowShellPolicy(selectedAgents, options = {}) {
+  const platform = options.platform || process.platform;
+
+  if (!needsWorkflowRuntimeAssets(selectedAgents)) {
+    return {
+      required: false,
+      available: true,
+      platform,
+      policy: platform === 'win32' ? 'git-bash' : 'system-shell',
+      command: platform === 'win32' ? null : 'sh',
+      message: ''
+    };
+  }
+
+  const shellOptions = { platform };
+  if (Object.hasOwn(options, 'candidates')) {
+    shellOptions.candidates = options.candidates;
+  }
+  if (typeof options._exists === 'function') {
+    shellOptions._exists = options._exists;
+  }
+  if (typeof options._canExecute === 'function') {
+    shellOptions._canExecute = options._canExecute;
+  }
+
+  return {
+    required: true,
+    ...resolveShellRuntime(shellOptions)
+  };
+}
+
+function ensureWorkflowShellPolicy(selectedAgents, options = {}) {
+  const shellPolicy = resolveWorkflowShellPolicy(selectedAgents, options);
+
+  if (shellPolicy.required && shellPolicy.platform === 'win32' && !shellPolicy.available) {
+    throw new Error(
+      shellPolicy.message || 'Git Bash is required on Windows for Forge workflow helper scripts.'
+    );
+  }
+
+  return shellPolicy;
+}
+
+
+
+function createSymlinkOrCopy(source, target, options = {}) {
+  const fullSource = path.resolve(projectRoot, source);
+  const fullTarget = path.resolve(projectRoot, target);
+  const resolvedProjectRoot = path.resolve(projectRoot);
+
+  // SECURITY: Prevent path traversal attacks
+  if (!fullSource.startsWith(resolvedProjectRoot)) {
+    console.error(`  ✗ Security: Source path escape blocked: ${source}`);
+    return '';
+  }
+  if (!fullTarget.startsWith(resolvedProjectRoot)) {
+    console.error(`  ✗ Security: Target path escape blocked: ${target}`);
+    return '';
+  }
+
+  // Delegate to lib/symlink-utils after security validation
+  return libCreateSymlinkOrCopy(fullSource, fullTarget, options);
+}
+
+function shouldLinkAgentsMd(agent) {
+  if (!agent?.linkFile) return false;
+  return !['copilot', 'opencode'].includes(agent.customSetup);
+}
+
+
+
+function stripFrontmatter(content) {
+  return fileUtils.stripFrontmatter(content);
+}
+
+// Read existing .env.local
+
+
+// Read existing .env.local (thin wrapper preserved for potential external callers)
+function _readEnvFile() {
+  return fileUtils.readEnvFile(projectRoot);
+}
+
+// Parse .env.local and return key-value pairs
+
+
+// Parse .env.local and return key-value pairs
+function parseEnvFile() {
+  return fileUtils.parseEnvFile(projectRoot);
+}
+
+// Write or update .env.local - PRESERVES existing values
+
+
+// Write or update .env.local - PRESERVES existing values
+function writeEnvTokens(tokens, preserveExisting = true) {
+  return fileUtils.writeEnvTokens(tokens, projectRoot, preserveExisting);
+}
+
+// Detect existing project installation status
+// Smart merge for AGENTS.md - extracted to lib/smart-merge.js for testability
+
+// Helper function for yes/no prompts with validation
+// askYesNo — wrapper around lib/ui-utils.js that passes NON_INTERACTIVE global
+
+
+// Detect existing project installation status
+// Smart merge for AGENTS.md - extracted to lib/smart-merge.js for testability
+
+// Helper function for yes/no prompts with validation
+// askYesNo — wrapper around lib/ui-utils.js that passes NON_INTERACTIVE global
+async function askYesNo(question, prompt, defaultNo = true) {
+  return _askYesNoBase(question, prompt, defaultNo, NON_INTERACTIVE);
+}
+
+
+
+async function detectProjectStatus() {
+  const status = {
+    type: 'fresh', // 'fresh', 'upgrade', or 'partial'
+    hasAgentsMd: fs.existsSync(path.join(projectRoot, 'AGENTS.md')),
+    hasClaudeMd: fs.existsSync(path.join(projectRoot, 'CLAUDE.md')),
+    hasClaudeCommands: fs.existsSync(path.join(projectRoot, '.claude/commands')),
+    hasEnvLocal: fs.existsSync(path.join(projectRoot, '.env.local')),
+    existingEnvVars: {},
+    agentsMdSize: 0,
+    claudeMdSize: 0,
+    agentsMdLines: 0,
+    claudeMdLines: 0,
+    // Project tools status
+    hasBeads: isBeadsInitialized(),
+    hasSkills: isSkillsInitialized(),
+    beadsInstallType: checkForBeads(),
+    skillsInstallType: checkForSkills(),
+    // Enhanced: Auto-detected project context
+    autoDetected: null
+  };
+
+  // Get file sizes and line counts for context warnings
+  if (status.hasAgentsMd) {
+    const agentsPath = path.join(projectRoot, 'AGENTS.md');
+    const stats = fs.statSync(agentsPath);
+    const content = fs.readFileSync(agentsPath, 'utf8');
+    status.agentsMdSize = stats.size;
+    status.agentsMdLines = content.split('\n').length;
+  }
+
+  if (status.hasClaudeMd) {
+    const claudePath = path.join(projectRoot, 'CLAUDE.md');
+    const stats = fs.statSync(claudePath);
+    const content = fs.readFileSync(claudePath, 'utf8');
+    status.claudeMdSize = stats.size;
+    status.claudeMdLines = content.split('\n').length;
+  }
+
+  // Determine installation type
+  if (status.hasAgentsMd && status.hasClaudeCommands) {
+    status.type = 'upgrade'; // Full forge installation exists
+  } else if (status.hasClaudeCommands || status.hasEnvLocal) {
+    status.type = 'partial'; // Agent-specific files exist (not just base files from postinstall)
+  }
+  // else: 'fresh' - new installation (or just postinstall baseline with AGENTS.md)
+
+  // Parse existing env vars if .env.local exists
+  if (status.hasEnvLocal) {
+    status.existingEnvVars = parseEnvFile();
+  }
+
+  // Enhanced: Auto-detect project context (framework, language, stage, CI/CD)
+  try {
+    status.autoDetected = await projectDiscovery.autoDetect(projectRoot);
+    // Save context to .forge/context.json
+    await projectDiscovery.saveContext(status.autoDetected, projectRoot);
+  } catch (error) {
+    // Auto-detection is optional - don't fail setup if it errors
+    console.log('  Note: Auto-detection skipped (error:', error.message, ')');
+    status.autoDetected = null;
+  }
+
+  return status;
+}
+
+// Detection helpers — delegated to lib/detection-utils.js
+
+
+// Detection helpers — delegated to lib/detection-utils.js
+function detectTestFramework(deps) { return detectionUtils.detectTestFramework(deps); }
+
+function detectLanguageFeatures(pkg) { return detectionUtils.detectLanguageFeatures(pkg, projectRoot); }
+
+function detectNextJs(deps) { return detectionUtils.detectNextJs(deps); }
+
+function detectNestJs(deps) { return detectionUtils.detectNestJs(deps); }
+
+function detectAngular(deps) { return detectionUtils.detectAngular(deps); }
+
+function detectVue(deps) { return detectionUtils.detectVue(deps); }
+
+function detectReact(deps) { return detectionUtils.detectReact(deps); }
+
+function detectExpress(deps, features) { return detectionUtils.detectExpress(deps, features); }
+
+function detectFastify(deps, features) { return detectionUtils.detectFastify(deps, features); }
+
+function detectSvelte(deps) { return detectionUtils.detectSvelte(deps); }
+
+function detectRemix(deps) { return detectionUtils.detectRemix(deps); }
+
+function detectAstro(deps) { return detectionUtils.detectAstro(deps); }
+
+function detectGenericNodeJs(pkg, deps, features) { return detectionUtils.detectGenericNodeJs(pkg, deps, features); }
+
+// Helper: Detect generic JavaScript/TypeScript project (fallback)
+
+
+// Helper: Detect generic JavaScript/TypeScript project (fallback)
+function detectGenericProject(deps, features) {
+  const hasVite = deps.vite;
+  const hasWebpack = deps.webpack;
+
+  // Determine build tool without nested ternary
+  let buildTool = 'npm';
+  if (hasVite) {
+    buildTool = 'vite';
+  } else if (hasWebpack) {
+    buildTool = 'webpack';
+  }
+
+  return {
+    framework: features.typescript ? 'TypeScript' : 'JavaScript',
+    frameworkConfidence: 60,
+    projectType: 'library',
+    buildTool,
+    testFramework: detectTestFramework(deps)
+  };
+}
+
+/**
+ * Read package.json from project root
+ * @returns {object|null} Parsed package.json or null if not found
+ */
+
+
+/**
+ * Read package.json from project root
+ * @returns {object|null} Parsed package.json or null if not found
+ */
+function readPackageJson() {
+  try {
+    const pkgPath = path.join(projectRoot, 'package.json');
+    if (!fs.existsSync(pkgPath)) {
+      return null;
+    }
+    return JSON.parse(fs.readFileSync(pkgPath, 'utf8'));
+  } catch (_err) { // NOSONAR - S2486: Returns null on invalid/missing package.json
+    return null;
+  }
+}
+
+// Detect project type from package.json
+
+
+// Detect project type from package.json
+function detectProjectType() {
+  const detection = {
+    hasPackageJson: false,
+    framework: null,
+    frameworkConfidence: 0,
+    language: 'javascript',
+    languageConfidence: 100,
+    projectType: null,
+    buildTool: null,
+    testFramework: null,
+    features: {
+      typescript: false,
+      monorepo: false,
+      docker: false,
+      cicd: false
+    }
+  };
+
+  const pkg = readPackageJson();
+  if (!pkg) return detection;
+
+  detection.hasPackageJson = true;
+
+  // Detect language features
+  detection.features = detectLanguageFeatures(pkg);
+  if (detection.features.typescript) {
+    detection.language = 'typescript';
+  }
+
+  // Framework detection with confidence scoring
+  const deps = { ...pkg.dependencies, ...pkg.devDependencies };
+
+  // Try framework detectors in priority order
+  const frameworkResult =
+    detectNextJs(deps) ||
+    detectNestJs(deps) ||
+    detectAngular(deps) ||
+    detectVue(deps) ||
+    detectReact(deps) ||
+    detectExpress(deps, detection.features) ||
+    detectFastify(deps, detection.features) ||
+    detectSvelte(deps) ||
+    detectRemix(deps) ||
+    detectAstro(deps) ||
+    detectGenericNodeJs(pkg, deps, detection.features) ||
+    detectGenericProject(deps, detection.features);
+
+  // Merge framework detection results
+  if (frameworkResult) {
+    Object.assign(detection, frameworkResult);
+  }
+
+  return detection;
+}
+
+// Display project detection results
+
+
+// Display project detection results
+function displayProjectType(detection) {
+  if (!detection.hasPackageJson) return;
+
+  console.log('');
+  console.log('  📦 Project Detection:');
+
+  if (detection.framework) {
+    const confidence = detection.frameworkConfidence >= 90 ? '✓' : '~';
+    console.log(`     Framework: ${detection.framework} ${confidence}`);
+  }
+
+  if (detection.projectType) {
+    console.log(`     Type: ${detection.projectType}`);
+  }
+
+  if (detection.buildTool) {
+    console.log(`     Build: ${detection.buildTool}`);
+  }
+
+  if (detection.testFramework) {
+    console.log(`     Tests: ${detection.testFramework}`);
+  }
+
+  const features = [];
+  if (detection.features.typescript) features.push('TypeScript');
+  if (detection.features.monorepo) features.push('Monorepo');
+  if (detection.features.docker) features.push('Docker');
+  if (detection.features.cicd) features.push('CI/CD');
+
+  if (features.length > 0) {
+    console.log(`     Features: ${features.join(', ')}`);
+  }
+}
+
+// Generate framework-specific tips
+
+
+// Generate framework-specific tips
+function generateFrameworkTips(detection) {
+  const tips = {
+    'Next.js': [
+      '- Use `npm run dev` for development with hot reload',
+      '- Server components are default in App Router',
+      '- API routes live in `app/api/` or `pages/api/`'
+    ],
+    'React': [
+      '- Prefer functional components with hooks',
+      '- Use `React.memo()` for expensive components',
+      '- State management: Context API or external library'
+    ],
+    'Vue.js': [
+      '- Use Composition API for better TypeScript support',
+      '- `<script setup>` is the recommended syntax',
+      '- Pinia is the official state management'
+    ],
+    'Angular': [
+      '- Use standalone components (Angular 14+)',
+      '- Signals for reactive state (Angular 16+)',
+      '- RxJS for async operations'
+    ],
+    'NestJS': [
+      '- Dependency injection via decorators',
+      '- Use `@nestjs/config` for environment variables',
+      '- Guards for authentication, Interceptors for logging'
+    ],
+    'Express': [
+      '- Use middleware for cross-cutting concerns',
+      '- Error handling with next(err)',
+      '- Consider Helmet.js for security headers'
+    ],
+    'Fastify': [
+      '- Schema-based validation with JSON Schema',
+      '- Plugins for reusable functionality',
+      '- Async/await by default'
+    ],
+    'SvelteKit': [
+      '- File-based routing in `src/routes/`',
+      '- Server-side rendering by default',
+      '- Form actions for mutations'
+    ],
+    'Nuxt': [
+      '- Auto-imports for components and composables',
+      '- `useAsyncData()` for data fetching',
+      '- Nitro server engine for deployment'
+    ],
+    'Remix': [
+      '- Loaders for data fetching',
+      '- Actions for mutations',
+      '- Progressive enhancement by default'
+    ],
+    'Astro': [
+      '- Zero JS by default',
+      '- Use client:* directives for interactivity',
+      '- Content collections for type-safe content'
+    ]
+  };
+
+  return tips[detection.framework] || [];
+}
+
+// Update AGENTS.md with project type metadata
+
+
+// Update AGENTS.md with project type metadata
+function updateAgentsMdWithProjectType(detection) {
+  const agentsPath = path.join(projectRoot, 'AGENTS.md');
+  if (!fs.existsSync(agentsPath)) return;
+
+  let content = fs.readFileSync(agentsPath, 'utf-8');
+
+  // Find the project description line (line 3)
+  const lines = content.split('\n');
+  let insertIndex = -1;
+
+  for (let i = 0; i < Math.min(lines.length, 10); i++) {
+    if (lines[i].startsWith('This is a ')) {
+      insertIndex = i + 1;
+      break;
+    }
+  }
+
+  if (insertIndex === -1) return;
+
+  // Build metadata section
+  const metadata = [];
+  metadata.push('');
+  if (detection.framework) {
+    metadata.push(`**Framework**: ${detection.framework}`);
+  }
+  if (detection.language && detection.language !== 'javascript') {
+    metadata.push(`**Language**: ${detection.language}`);
+  }
+  if (detection.projectType) {
+    metadata.push(`**Type**: ${detection.projectType}`);
+  }
+  if (detection.buildTool) {
+    metadata.push(`**Build**: \`${detection.buildTool}\``);
+  }
+  if (detection.testFramework) {
+    metadata.push(`**Tests**: ${detection.testFramework}`);
+  }
+
+  // Add framework-specific tips
+  const tips = generateFrameworkTips(detection);
+  if (tips.length > 0) {
+    metadata.push('', '**Framework conventions**:', ...tips);
+  }
+
+  // Insert metadata
+  lines.splice(insertIndex, 0, ...metadata);
+
+  fs.writeFileSync(agentsPath, lines.join('\n'), 'utf-8');
+}
+
+// Helper: Calculate estimated tokens (rough: ~4 chars per token)
+
+
+// Helper: Calculate estimated tokens (rough: ~4 chars per token)
+function estimateTokens(bytes) {
+  return Math.ceil(bytes / 4);
+}
+
+// Helper: Create instruction files result object
+
+
+// Helper: Create instruction files result object
+function createInstructionFilesResult(createAgentsMd = false, createClaudeMd = false, skipAgentsMd = false, skipClaudeMd = false) {
+  return {
+    createAgentsMd,
+    createClaudeMd,
+    skipAgentsMd,
+    skipClaudeMd
+  };
+}
+
+// Helper: Handle scenario where both AGENTS.md and CLAUDE.md exist
+
+
+// Helper: Handle scenario where both AGENTS.md and CLAUDE.md exist
+async function handleBothFilesExist(question, projectStatus) {
+  const totalLines = projectStatus.agentsMdLines + projectStatus.claudeMdLines;
+  const totalTokens = estimateTokens(projectStatus.agentsMdSize + projectStatus.claudeMdSize);
+
+  console.log('');
+  console.log('⚠️  WARNING: Multiple Instruction Files Detected');
+  console.log('='.repeat(60));
+  console.log(`  AGENTS.md:  ${projectStatus.agentsMdLines} lines (~${estimateTokens(projectStatus.agentsMdSize)} tokens)`);
+  console.log(`  CLAUDE.md:  ${projectStatus.claudeMdLines} lines (~${estimateTokens(projectStatus.claudeMdSize)} tokens)`);
+  console.log(`  Total:      ${totalLines} lines (~${totalTokens} tokens)`);
+  console.log('');
+  console.log('  ⚠️  Claude Code reads BOTH files on every request');
+  console.log('  ⚠️  This increases context usage and costs');
+  console.log('');
+  console.log('  Options:');
+  console.log('  1) Keep CLAUDE.md only (recommended for Claude Code only)');
+  console.log('  2) Keep AGENTS.md only (recommended for multi-agent users)');
+  console.log('  3) Keep both (higher context usage)');
+  console.log('');
+
+  while (true) {
+    const choice = await question('Your choice (1/2/3) [2]: ');
+    const normalized = choice.trim() || '2';
+
+    if (normalized === '1') {
+      console.log('  ✓ Will keep CLAUDE.md, remove AGENTS.md');
+      return createInstructionFilesResult(false, false, true, false);
+    } else if (normalized === '2') {
+      console.log('  ✓ Will keep AGENTS.md, remove CLAUDE.md');
+      return createInstructionFilesResult(false, false, false, true);
+    } else if (normalized === '3') {
+      console.log('  ✓ Will keep both files (context: ~' + totalTokens + ' tokens)');
+      return createInstructionFilesResult(false, false, false, false);
+    } else {
+      console.log('  Please enter 1, 2, or 3');
+    }
+  }
+}
+
+// Helper: Handle scenario where only CLAUDE.md exists
+
+
+// Helper: Handle scenario where only CLAUDE.md exists
+async function handleOnlyClaudeMdExists(question, projectStatus, hasOtherAgents) {
+  if (hasOtherAgents) {
+    console.log('');
+    console.log('📋 Found existing CLAUDE.md (' + projectStatus.claudeMdLines + ' lines)');
+    console.log('   You selected multiple agents. Recommendation:');
+    console.log('   → Migrate to AGENTS.md (works with all agents)');
+    console.log('');
+
+    const migrate = await askYesNo(question, 'Migrate CLAUDE.md to AGENTS.md?', false);
+    if (migrate) {
+      console.log('  ✓ Will migrate content to AGENTS.md');
+      return createInstructionFilesResult(true, false, false, true);
+    } else {
+      console.log('  ✓ Will keep CLAUDE.md and create AGENTS.md');
+      return createInstructionFilesResult(true, false, false, false);
+    }
+  } else {
+    // Claude Code only - keep CLAUDE.md
+    console.log('  ✓ Keeping existing CLAUDE.md');
+    return createInstructionFilesResult(false, false, false, false);
+  }
+}
+
+// Helper: Handle scenario where only AGENTS.md exists
+
+
+// Helper: Handle scenario where only AGENTS.md exists
+async function handleOnlyAgentsMdExists(question, projectStatus, hasClaude, hasOtherAgents) {
+  if (hasClaude && !hasOtherAgents) {
+    console.log('');
+    console.log('📋 Found existing AGENTS.md (' + projectStatus.agentsMdLines + ' lines)');
+    console.log('   You selected Claude Code only. Options:');
+    console.log('   1) Keep AGENTS.md (works fine)');
+    console.log('   2) Rename to CLAUDE.md (Claude-specific naming)');
+    console.log('');
+
+    const rename = await askYesNo(question, 'Rename to CLAUDE.md?', true);
+    if (rename) {
+      console.log('  ✓ Will rename to CLAUDE.md');
+      return createInstructionFilesResult(false, true, true, false);
+    } else {
+      console.log('  ✓ Keeping AGENTS.md');
+      return createInstructionFilesResult(false, false, false, false);
+    }
+  } else {
+    // Multi-agent or other agents - keep AGENTS.md
+    console.log('  ✓ Keeping existing AGENTS.md');
+    return createInstructionFilesResult(false, false, false, false);
+  }
+}
+
+// Helper: Handle scenario where no instruction files exist (fresh install)
+
+
+// Helper: Handle scenario where no instruction files exist (fresh install)
+function handleNoFilesExist(hasClaude, hasOtherAgents) {
+  if (hasClaude && !hasOtherAgents) {
+    // Claude Code only → create CLAUDE.md
+    console.log('  ✓ Will create CLAUDE.md (Claude Code specific)');
+    return createInstructionFilesResult(false, true, false, false);
+  } else if (!hasClaude && hasOtherAgents) {
+    // Other agents only → create AGENTS.md
+    console.log('  ✓ Will create AGENTS.md (universal)');
+    return createInstructionFilesResult(true, false, false, false);
+  } else {
+    // Multiple agents including Claude → create AGENTS.md + reference CLAUDE.md
+    console.log('  ✓ Will create AGENTS.md (main) + CLAUDE.md (reference)');
+    return createInstructionFilesResult(true, true, false, false);
+  }
+}
+
+// Smart file selection with context warnings
+// @private - Currently unused, reserved for future interactive setup flow
+
+
+// Smart file selection with context warnings
+// @private - Currently unused, reserved for future interactive setup flow
+async function _handleInstructionFiles(rl, question, selectedAgents, projectStatus) {
+  const hasClaude = selectedAgents.some(a => a.key === 'claude');
+  const hasOtherAgents = selectedAgents.some(a => a.key !== 'claude');
+
+  // Scenario 1: Both files exist (potential context bloat)
+  if (projectStatus.hasAgentsMd && projectStatus.hasClaudeMd) {
+    return await handleBothFilesExist(question, projectStatus);
+  }
+
+  // Scenario 2: Only CLAUDE.md exists
+  if (projectStatus.hasClaudeMd && !projectStatus.hasAgentsMd) {
+    return await handleOnlyClaudeMdExists(question, projectStatus, hasOtherAgents);
+  }
+
+  // Scenario 3: Only AGENTS.md exists
+  if (projectStatus.hasAgentsMd && !projectStatus.hasClaudeMd) {
+    return await handleOnlyAgentsMdExists(question, projectStatus, hasClaude, hasOtherAgents);
+  }
+
+  // Scenario 4: Neither file exists (fresh install)
+  return handleNoFilesExist(hasClaude, hasOtherAgents);
+}
+
+// Prompt for code review tool selection - extracted to reduce cognitive complexity
+
+
+// Prompt for code review tool selection - extracted to reduce cognitive complexity
+async function promptForCodeReviewTool(question) {
+  console.log('');
+  console.log('Code Review Tool');
+  console.log('----------------');
+  console.log('Select your code review integration:');
+  console.log('');
+  console.log('  1) GitHub Code Quality (FREE, built-in) [RECOMMENDED]');
+  console.log('     Zero setup - uses GitHub\'s built-in code quality features');
+  console.log('');
+  console.log('  2) CodeRabbit (FREE for open source)');
+  console.log('     AI-powered reviews - install GitHub App at https://coderabbit.ai');
+  console.log('');
+  console.log('  3) Greptile (Paid - $99+/mo)');
+  console.log('     Enterprise code review - https://greptile.com');
+  console.log('');
+  console.log('  4) Skip code review integration');
+  console.log('');
+
+  const choice = await question('Select [1]: ') || '1';
+  const tokens = {};
+
+  switch (choice) {
+    case '1': {
+      tokens['CODE_REVIEW_TOOL'] = 'github-code-quality';
+      console.log('  ✓ Using GitHub Code Quality (FREE)');
+      break;
+    }
+    case '2': {
+      tokens['CODE_REVIEW_TOOL'] = 'coderabbit';
+      console.log('  ✓ Using CodeRabbit - Install the GitHub App to activate');
+      console.log('     https://coderabbit.ai');
+      break;
+    }
+    case '3': {
+      const greptileKey = await question('  Enter Greptile API key: ');
+      if (greptileKey?.trim()) {
+        tokens['CODE_REVIEW_TOOL'] = 'greptile';
+        tokens['GREPTILE_API_KEY'] = greptileKey.trim();
+        console.log('  ✓ Greptile configured');
+      } else {
+        tokens['CODE_REVIEW_TOOL'] = 'none';
+        console.log('  Skipped - No API key provided');
+      }
+      break;
+    }
+    default: {
+      tokens['CODE_REVIEW_TOOL'] = 'none';
+      console.log('  Skipped code review integration');
+    }
+  }
+
+  return tokens;
+}
+
+// Prompt for code quality tool selection - extracted to reduce cognitive complexity
+
+
+// Prompt for code quality tool selection - extracted to reduce cognitive complexity
+async function promptForCodeQualityTool(question) {
+  console.log('');
+  console.log('Code Quality Tool');
+  console.log('-----------------');
+  console.log('Select your code quality/security scanner:');
+  console.log('');
+  console.log('  1) ESLint only (FREE, built-in) [RECOMMENDED]');
+  console.log('     No external server required - uses project\'s linting');
+  console.log('');
+  console.log('  2) SonarCloud (50k LoC free, cloud-hosted)');
+  console.log('     Get token: https://sonarcloud.io/account/security');
+  console.log('');
+  console.log('  3) SonarQube Community (FREE, self-hosted, unlimited LoC)');
+  console.log('     Run: docker run -d --name sonarqube -p 9000:9000 sonarqube:community');
+  console.log('');
+  console.log('  4) Skip code quality integration');
+  console.log('');
+
+  const choice = await question('Select [1]: ') || '1';
+  const tokens = {};
+
+  switch (choice) {
+    case '1': {
+      tokens['CODE_QUALITY_TOOL'] = 'eslint';
+      console.log('  ✓ Using ESLint (built-in)');
+      break;
+    }
+    case '2': {
+      const sonarToken = await question('  Enter SonarCloud token: ');
+      const sonarOrg = await question('  Enter SonarCloud organization: ');
+      const sonarProject = await question('  Enter SonarCloud project key: ');
+      if (sonarToken?.trim()) {
+        tokens['CODE_QUALITY_TOOL'] = 'sonarcloud';
+        tokens['SONAR_TOKEN'] = sonarToken.trim();
+        if (sonarOrg) tokens['SONAR_ORGANIZATION'] = sonarOrg.trim();
+        if (sonarProject) tokens['SONAR_PROJECT_KEY'] = sonarProject.trim();
+        console.log('  ✓ SonarCloud configured');
+      } else {
+        tokens['CODE_QUALITY_TOOL'] = 'eslint';
+        console.log('  Falling back to ESLint');
+      }
+      break;
+    }
+    case '3': {
+      console.log('');
+      console.log('  SonarQube Self-Hosted Setup:');
+      console.log('  docker run -d --name sonarqube -p 9000:9000 sonarqube:community');
+      console.log('  Access: http://localhost:9000 (admin/admin)');
+      console.log('');
+      const sqUrl = await question('  Enter SonarQube URL [http://localhost:9000]: ') || 'http://localhost:9000';
+      const sqToken = await question('  Enter SonarQube token (optional): ');
+      tokens['CODE_QUALITY_TOOL'] = 'sonarqube';
+      tokens['SONARQUBE_URL'] = sqUrl;
+      if (sqToken?.trim()) {
+        tokens['SONARQUBE_TOKEN'] = sqToken.trim();
+      }
+      console.log('  ✓ SonarQube self-hosted configured');
+      break;
+    }
+    default: {
+      tokens['CODE_QUALITY_TOOL'] = 'none';
+      console.log('  Skipped code quality integration');
+    }
+  }
+
+  return tokens;
+}
+
+// Prompt for research tool selection - extracted to reduce cognitive complexity
+
+
+// Prompt for research tool selection - extracted to reduce cognitive complexity
+async function promptForResearchTool(question) {
+  console.log('');
+  console.log('Research Tool');
+  console.log('-------------');
+  console.log('Select your research tool for /research stage:');
+  console.log('');
+  console.log('  1) Manual research only [DEFAULT]');
+  console.log('     Use web browser and codebase exploration');
+  console.log('');
+  console.log('  2) Parallel AI (comprehensive web research)');
+  console.log('     Get key: https://platform.parallel.ai');
+  console.log('');
+
+  const choice = await question('Select [1]: ') || '1';
+  const tokens = {};
+
+  if (choice === '2') {
+    const parallelKey = await question('  Enter Parallel AI API key: ');
+    if (parallelKey?.trim()) {
+      tokens['PARALLEL_API_KEY'] = parallelKey.trim();
+      console.log('  ✓ Parallel AI configured');
+    } else {
+      console.log('  Skipped - No API key provided');
+    }
+  } else {
+    console.log('  ✓ Using manual research');
+  }
+
+  return tokens;
+}
+
+// Helper: Check existing service configuration - extracted to reduce cognitive complexity
+
+
+// Helper: Check existing service configuration - extracted to reduce cognitive complexity
+async function checkExistingServiceConfig(question, projectStatus) {
+  const existingEnvVars = projectStatus?.existingEnvVars || parseEnvFile();
+  const hasCodeReviewTool = existingEnvVars.CODE_REVIEW_TOOL;
+  const hasCodeQualityTool = existingEnvVars.CODE_QUALITY_TOOL;
+  const hasExistingConfig = hasCodeReviewTool || hasCodeQualityTool;
+
+  if (!hasExistingConfig) {
+    return true; // No existing config, proceed with configuration
+  }
+
+  console.log('External services already configured:');
+  if (hasCodeReviewTool) {
+    console.log(`  - CODE_REVIEW_TOOL: ${hasCodeReviewTool}`);
+  }
+  if (hasCodeQualityTool) {
+    console.log(`  - CODE_QUALITY_TOOL: ${hasCodeQualityTool}`);
+  }
+  console.log('');
+
+  const reconfigure = await askYesNo(question, 'Reconfigure external services?', true);
+  if (!reconfigure) {
+    console.log('');
+    console.log('Keeping existing configuration.');
+    return false; // Skip configuration
+  }
+  console.log('');
+  return true; // Proceed with configuration
+}
+
+// Helper: Display Context7 MCP status for selected agents - extracted to reduce cognitive complexity
+
+
+// Helper: Display Context7 MCP status for selected agents - extracted to reduce cognitive complexity
+function displayMcpStatus(selectedAgents) {
+  console.log('');
+  console.log('Context7 MCP - Library Documentation');
+  console.log('-------------------------------------');
+  console.log('Provides up-to-date library docs for AI coding agents.');
+  console.log('');
+
+  // Show what was/will be auto-installed
+  if (selectedAgents.includes('claude')) {
+    console.log('  ✓ Auto-installed for Claude Code (.mcp.json)');
+  }
+  // Show manual setup instructions for GUI-based agents
+  const manualMcpMap = {
+    cursor: 'Cursor: Configure via Cursor Settings > MCP',
+    cline: 'Cline: Install via MCP Marketplace',
+  };
+  const needsManualMcp = Object.entries(manualMcpMap)
+    .filter(([key]) => selectedAgents.includes(key))
+    .map(([, msg]) => msg);
+
+  if (needsManualMcp.length > 0) {
+    needsManualMcp.forEach(msg => console.log(`  ! ${msg}`));
+    console.log('');
+    console.log('  Package: @upstash/context7-mcp@latest');
+    console.log('  Docs: https://github.com/upstash/context7-mcp');
+  }
+}
+
+// Helper: Display env token write results - extracted to reduce cognitive complexity
+
+
+// Helper: Display env token write results - extracted to reduce cognitive complexity
+function displayEnvTokenResults(added, preserved) {
+  console.log('');
+  if (preserved.length > 0) {
+    console.log('Preserved existing values:');
+    preserved.forEach(key => {
+      console.log(`  - ${key} already configured - keeping existing value`);
+    });
+    console.log('');
+  }
+  if (added.length > 0) {
+    console.log('Added new configuration:');
+    added.forEach(key => {
+      console.log(`  - ${key}`);
+    });
+    console.log('');
+  }
+  console.log('Configuration saved to .env.local');
+  console.log('Note: .env.local has been added to .gitignore');
+}
+
+// Configure external services interactively
+
+
+// Configure external services interactively
+async function configureExternalServices(rl, question, selectedAgents = [], projectStatus = null) { // NOSONAR — Extracted as-is from bin/forge.js; complexity reduction deferred
+  console.log('');
+  console.log('==============================================');
+  console.log('  External Services Configuration');
+  console.log('==============================================');
+  console.log('');
+
+  // Check existing configuration
+  const shouldContinue = await checkExistingServiceConfig(question, projectStatus);
+  if (!shouldContinue) {
+    return;
+  }
+
+  console.log('Would you like to configure external services?');
+  console.log('(You can also add them later to .env.local)');
+  console.log('');
+
+  const configure = await askYesNo(question, 'Configure external services?', false);
+
+  if (!configure) {
+    console.log('');
+    console.log('Skipping external services. You can configure them later by editing .env.local');
+    return;
+  }
+
+  // Prompt for each service and collect tokens
+  const tokens = {};
+
+  // CODE REVIEW TOOL
+  Object.assign(tokens, await promptForCodeReviewTool(question));
+
+  // CODE QUALITY TOOL
+  Object.assign(tokens, await promptForCodeQualityTool(question));
+
+  // RESEARCH TOOL
+  Object.assign(tokens, await promptForResearchTool(question));
+
+  // Context7 MCP - Library Documentation
+  displayMcpStatus(selectedAgents);
+
+  // Save package manager preference
+  tokens['PKG_MANAGER'] = PKG_MANAGER;
+
+  // Write all tokens to .env.local (preserving existing values)
+  const { added, preserved } = writeEnvTokens(tokens, true);
+  displayEnvTokenResults(added, preserved);
+
+  // GitHub-Beads issue sync setup
+  console.log('');
+  const enableSync = await askYesNo(question, 'Enable GitHub ↔ Beads issue sync?', true);
+  if (enableSync) {
+    try {
+      const result = await scaffoldGithubBeadsSync(projectRoot, packageDir);
+      for (const f of result.created) {
+        console.log(`  Created: ${f}`);
+      }
+      for (const f of result.skipped) {
+        console.log(`  Skipped: ${f} (already exists)`);
+      }
+
+      // PAT setup guidance for Beads sync (non-fatal)
+      // Skip if --sync flag is set — handleSyncScaffold will handle PAT setup
+      if (!SYNC_ENABLED) {
+        try {
+          const patResult = setupPAT(projectRoot, { interactive: !NON_INTERACTIVE });
+          if (patResult.success) {
+            console.log('  ✓ Beads sync PAT configured');
+          } else if (patResult.reminder) {
+            console.log(`  ℹ ${patResult.reminder}`);
+          } else if (patResult.instructions) {
+            console.log(`  ℹ ${patResult.instructions.split('\n')[0]}`);
+          }
+        } catch (_patErr) { // NOSONAR — best-effort PAT setup, non-fatal
+          // PAT setup is best-effort — don't block sync scaffold
+        }
+      }
+    } catch (err) {
+      console.error(`  Error scaffolding GitHub-Beads sync: ${err.message}`);
+    }
+  }
+}
+
+// Display the Forge banner
+
+
+// Display the Forge banner
+function showBanner(subtitle = 'Universal AI Agent Workflow') {
+  console.log('');
+  console.log('  ███████╗ ██████╗ ██████╗  ██████╗ ███████╗');
+  console.log('  ██╔════╝██╔═══██╗██╔══██╗██╔════╝ ██╔════╝');
+  console.log('  █████╗  ██║   ██║██████╔╝██║  ███╗█████╗  ');
+  console.log('  ██╔══╝  ██║   ██║██╔══██╗██║   ██║██╔══╝  ');
+  console.log('  ██║     ╚██████╔╝██║  ██║╚██████╔╝███████╗');
+  console.log('  ╚═╝      ╚═════╝ ╚═╝  ╚═╝ ╚═════╝ ╚══════╝');
+  console.log(`  v${VERSION}`);
+  console.log('');
+  if (subtitle) {
+    console.log(`  ${subtitle}`);
+  }
+}
+
+/**
+ * Creates a directory on first use and prints a one-time purpose note.
+ * Delegates to lib/file-utils.js.
+ * @param {string} dir - Absolute path to the directory to create.
+ * @param {string} purpose - Human-readable purpose description.
+ * @returns {string|null} Purpose message if created, null if already existed.
+ */
+
+
+/**
+ * Creates a directory on first use and prints a one-time purpose note.
+ * Delegates to lib/file-utils.js.
+ * @param {string} dir - Absolute path to the directory to create.
+ * @param {string} purpose - Human-readable purpose description.
+ * @returns {string|null} Purpose message if created, null if already existed.
+ */
+function ensureDirWithNote(dir, purpose) { // eslint-disable-line no-unused-vars -- exported via module.exports
+  return fileUtils.ensureDirWithNote(dir, purpose);
+}
+
+// Setup core documentation and directories
+
+
+// Setup core documentation and directories
+function setupCoreDocs() {
+  // docs/planning/ and docs/research/ are created lazily on first use
+  // by /plan Phase 1 and Phase 2 respectively, via ensureDirWithNote().
+  // TEMPLATE.md and PROGRESS.md are also deferred to first use.
+
+  // Copy essential docs (TOOLCHAIN.md, VALIDATION.md) to consumer's docs/forge/
+  const result = copyEssentialDocs(projectRoot, packageDir);
+  for (const f of result.created) {
+    console.log(`  Created: ${f}`);
+  }
+  for (const f of result.skipped) {
+    if (VERBOSE_MODE) {
+      console.log(`  Skipped: ${f} (already exists)`);
+    }
+  }
+}
+
+// Minimal installation (postinstall)
+
+
+// Minimal installation (postinstall)
+function minimalInstall() {
+  // Check if this looks like a project (has package.json)
+  const hasPackageJson = fs.existsSync(path.join(projectRoot, 'package.json'));
+
+  if (!hasPackageJson) {
+    console.log('');
+    console.log('  ✅ Forge installed successfully!');
+    console.log('');
+    console.log('  To set up in a project:');
+    console.log('    cd your-project');
+    console.log('    npx forge setup');
+    console.log('');
+    console.log('  Or specify a project directory:');
+    console.log('    npx forge setup --path ./my-project');
+    console.log('');
+    return;
+  }
+
+  showBanner();
+  console.log('');
+
+  // Setup core documentation
+  setupCoreDocs();
+
+  // Copy AGENTS.md (only if not exists - preserve user customizations in minimal install)
+  const agentsPath = path.join(projectRoot, 'AGENTS.md');
+  if (fs.existsSync(agentsPath)) {
+    console.log('  Skipped: AGENTS.md (already exists)');
+  } else {
+    const agentsSrc = path.join(packageDir, 'AGENTS.md');
+    if (copyFile(agentsSrc, 'AGENTS.md')) {
+      console.log('  Created: AGENTS.md (universal standard)');
+
+      // Detect project type and update AGENTS.md
+      const detection = detectProjectType();
+      if (detection.hasPackageJson) {
+        updateAgentsMdWithProjectType(detection);
+        displayProjectType(detection);
+      }
+    }
+  }
+
+  console.log('');
+  console.log('Minimal installation complete!');
+  console.log('');
+  console.log('To configure for your AI coding agents, run:');
+  console.log('');
+  console.log('  bun add -d lefthook      # Install git hooks (one-time)');
+  console.log('  bunx forge setup         # Interactive setup (agents + API tokens)');
+  console.log('');
+  console.log('Or specify agents directly:');
+  console.log('  bunx forge setup --agents claude,cursor');
+  console.log('  bunx forge setup --all');
+  console.log('');
+}
+
+// Helper: Setup Claude agent
+
+
+// Helper: Setup Claude agent
+function setupClaudeAgent(skipFiles = {}) {
+  // Copy commands from package (unless skipped)
+  if (skipFiles.claudeCommands) {
+    console.log('  Skipped: .claude/commands/ (keeping existing)');
+  } else {
+    const cmds = getWorkflowCommands();
+    let copied = 0;
+    cmds.forEach(cmd => {
+      const src = path.join(packageDir, `.claude/commands/${cmd}.md`);
+      if (copyFile(src, `.claude/commands/${cmd}.md`)) copied++;
+    });
+    console.log(`  Copied: ${copied} workflow commands`);
+  }
+
+  // Copy rules
+  const rulesSrc = path.join(packageDir, '.claude/rules/workflow.md');
+  copyFile(rulesSrc, '.claude/rules/workflow.md');
+
+  // Copy scripts
+  const scriptSrc = path.join(packageDir, '.claude/scripts/load-env.sh');
+  copyFile(scriptSrc, '.claude/scripts/load-env.sh');
+}
+
+// Helper: Setup Cursor agent
+
+
+// Helper: Setup Cursor agent
+async function setupCursorAgent() {
+  await generateCursorConfig(projectRoot, { overwrite: false });
+  console.log('  Created: Cursor native rules');
+}
+
+async function setupKiloAgent() {
+  await generateKiloConfig(projectRoot, { overwrite: false });
+  console.log('  Created: Kilo native workflow files');
+}
+
+async function setupCopilotAgent() {
+  await generateCopilotConfig(projectRoot, { overwrite: false });
+  console.log('  Created: Copilot native config');
+}
+
+async function setupOpenCodeAgent() {
+  await generateOpenCodeConfig(projectRoot, { overwrite: false });
+  console.log('  Created: OpenCode native config');
+}
+
+// Helper: Convert command to agent-specific format
+
+
+// Helper: Convert command to agent-specific format
+function convertCommandToAgentFormat(cmd, content, agent) {
+  let targetContent = content;
+  let targetFile = cmd;
+
+  if (agent.needsConversion) {
+    targetContent = stripFrontmatter(content);
+  }
+
+  if (agent.promptFormat) {
+    targetFile = cmd.replace('.md', '.prompt.md');
+    targetContent = stripFrontmatter(content);
+  }
+
+  return { targetFile, targetContent };
+}
+
+// Helper: Copy commands for agent
+
+
+// Helper: Copy commands for agent
+function copyAgentCommands(agent, claudeCommands) {
+  if (!claudeCommands) return;
+  if (!agent.needsConversion && !agent.copyCommands && !agent.promptFormat) return;
+
+  Object.entries(claudeCommands).forEach(([cmd, content]) => {
+    const { targetFile, targetContent } = convertCommandToAgentFormat(cmd, content, agent);
+    const targetDir = agent.dirs[0]; // First dir is commands/workflows
+    writeFile(`${targetDir}/${targetFile}`, targetContent);
+  });
+  console.log(`  Converted: ${Object.keys(claudeCommands).length} workflow commands`);
+}
+
+// Helper: Copy rules for agent
+
+
+// Helper: Copy rules for agent
+function copyAgentRules(agent) {
+  if (!agent.needsConversion) return;
+
+  const workflowMdPath = path.join(projectRoot, '.claude/rules/workflow.md');
+  if (!fs.existsSync(workflowMdPath)) return;
+
+  const rulesDir = agent.dirs.find(d => d.includes('/rules'));
+  if (!rulesDir) return;
+
+  const ruleContent = readFile(workflowMdPath);
+  if (ruleContent) {
+    writeFile(`${rulesDir}/workflow.md`, ruleContent);
+  }
+}
+
+// Helper: Create skill file for agent
+
+
+// Helper: Create skill file for agent
+function createAgentSkill(agent, agentKey) {
+  if (agentKey === 'codex') {
+    createCodexSkills();
+    return;
+  }
+
+  if (!agent.hasSkill) return;
+
+  const skillDir = agent.dirs.find(d => d.includes('/skills/'));
+  if (skillDir) {
+    writeFile(`${skillDir}/SKILL.md`, SKILL_CONTENT);
+    console.log('  Created: forge-workflow skill');
+  }
+}
+
+// Helper: Create Codex per-stage skills from canonical commands
+function createCodexSkills() {
+  const entries = listCodexSkillEntries(packageDir);
+
+  for (const entry of entries) {
+    writeFile(path.join(entry.dir, entry.filename), entry.content);
+  }
+
+  if (entries.length > 0) {
+    console.log(`  Created: Codex stage skills (${entries.length})`);
+  }
+}
+
+// Helper: Setup MCP config for Claude
+
+
+// Helper: Setup MCP config for Claude
+function setupClaudeMcpConfig() {
+  const mcpPath = path.join(projectRoot, '.mcp.json');
+  if (fs.existsSync(mcpPath)) {
+    console.log('  Skipped: .mcp.json already exists');
+    return;
+  }
+
+  const mcpConfig = {
+    mcpServers: {
+      context7: {
+        command: 'npx',
+        args: ['-y', '@upstash/context7-mcp@latest']
+      }
+    }
+  };
+  writeFile('.mcp.json', JSON.stringify(mcpConfig, null, 2));
+  console.log('  Created: .mcp.json with Context7 MCP');
+}
+
+// Helper: Create agent link file
+// When symlinkOnly is true (--symlink flag), skip copy fallback
+
+
+// Helper: Create agent link file
+// When symlinkOnly is true (--symlink flag), skip copy fallback
+function createAgentLinkFile(agent, symlinkOnly = false) {
+  if (!shouldLinkAgentsMd(agent)) return;
+
+  const result = createSymlinkOrCopy('AGENTS.md', agent.linkFile, { symlinkOnly });
+  if (result) {
+    console.log(`  ${result === 'linked' ? 'Linked' : 'Copied'}: ${agent.linkFile}`);
+  }
+}
+
+// Setup specific agent
+
+
+// Setup specific agent
+async function setupAgent(agentKey, claudeCommands, skipFiles = {}) {
+  const agent = AGENTS[agentKey];
+  if (!agent) return;
+
+  console.log(`\nSetting up ${agent.name}...`);
+  if (agent.supportStatus === 'deprecated') {
+    console.log(`  Warning: ${agent.name} is in deprecated compatibility mode; Forge will scaffold converted workflow files only.`);
+  }
+
+  // Create directories
+  agent.dirs.forEach(dir => ensureDir(dir));
+
+  // Handle agent-specific setup
+  if (agentKey === 'claude') {
+    setupClaudeAgent(skipFiles);
+  }
+
+  if (agent.customSetup === 'cursor') {
+    await setupCursorAgent();
+  }
+
+  if (agentKey === 'kilocode') {
+    await setupKiloAgent();
+  }
+
+  if (agentKey === 'copilot') {
+    await setupCopilotAgent();
+  }
+
+  if (agentKey === 'opencode') {
+    await setupOpenCodeAgent();
+  }
+
+  // Convert/copy commands
+  copyAgentCommands(agent, claudeCommands);
+
+  // Copy rules if needed
+  copyAgentRules(agent);
+
+  // Create SKILL.md or Codex stage skills
+  createAgentSkill(agent, agentKey);
+
+  // Setup MCP configs
+  if (agentKey === 'claude') {
+    setupClaudeMcpConfig();
+  }
+
+  // Create link file (SYMLINK_ONLY = --symlink flag disables copy fallback)
+  createAgentLinkFile(agent, SYMLINK_ONLY);
+}
+
+
+// =============================================
+// Helper Functions for Interactive Setup
+// =============================================
+
+/**
+ * Display existing installation status
+ */
+
+
+
+// =============================================
+// Helper Functions for Interactive Setup
+// =============================================
+
+/**
+ * Display existing installation status
+ */
+function displayInstallationStatus(projectStatus) {
+  if (projectStatus.type === 'fresh') return;
+
+  console.log('==============================================');
+  console.log('  Existing Installation Detected');
+  console.log('==============================================');
+  console.log('');
+
+  if (projectStatus.type === 'upgrade') {
+    console.log('Found existing Forge installation:');
+  } else {
+    console.log('Found partial installation:');
+  }
+
+  if (projectStatus.hasAgentsMd) console.log('  - AGENTS.md');
+  if (projectStatus.hasClaudeCommands) console.log('  - .claude/commands/');
+  if (projectStatus.hasEnvLocal) console.log('  - .env.local');
+  console.log('');
+}
+
+/**
+ * Handle AGENTS.md file without markers - offers 3 options
+ * Extracted to reduce cognitive complexity
+ */
+
+
+/**
+ * Handle AGENTS.md file without markers - offers 3 options
+ * Extracted to reduce cognitive complexity
+ */
+async function promptForAgentsMdWithoutMarkers(question, skipFiles, agentsPath) {
+  console.log('');
+  console.log('Found existing AGENTS.md without Forge markers.');
+  console.log('This file may contain your custom agent instructions.');
+  console.log('');
+  console.log('How would you like to proceed?');
+  console.log('  1. Intelligent merge (preserve your content + add Forge workflow)');
+  console.log('  2. Keep existing (skip Forge installation for this file)');
+  console.log('  3. Replace (backup created at AGENTS.md.backup)');
+  console.log('');
+
+  let validChoice = false;
+  while (!validChoice) {
+    const answer = await question('Your choice (1-3) [1]: ');
+    const choice = answer.trim() || '1';
+
+    if (choice === '1') {
+      // Intelligent merge
+      skipFiles.useSemanticMerge = true;
+      skipFiles.agentsMd = false;
+      console.log('  Will use intelligent merge (preserving your content)');
+      validChoice = true;
+    } else if (choice === '2') {
+      // Keep existing
+      skipFiles.agentsMd = true;
+      console.log('  Keeping existing AGENTS.md');
+      validChoice = true;
+    } else if (choice === '3') {
+      // Replace (backup first)
+      try {
+        fs.copyFileSync(agentsPath, agentsPath + '.backup');
+        console.log('  Backup created: AGENTS.md.backup');
+      } catch (err) {
+        console.log('  Warning: Could not create backup');
+        console.warn('Backup creation failed:', err.message);
+      }
+      skipFiles.agentsMd = false;
+      skipFiles.useSemanticMerge = false;
+      console.log('  Will replace AGENTS.md');
+      validChoice = true;
+    } else {
+      console.log('  Please enter 1, 2, or 3');
+    }
+  }
+}
+
+/**
+ * Prompt for file overwrite and update skipFiles
+ * Enhanced: For AGENTS.md without markers, offers intelligent merge option
+ */
+
+
+/**
+ * Prompt for file overwrite and update skipFiles
+ * Enhanced: For AGENTS.md without markers, offers intelligent merge option
+ */
+async function promptForFileOverwrite(question, fileType, exists, skipFiles) {
+  if (!exists) return;
+
+  const fileLabels = {
+    agentsMd: { prompt: 'Found existing AGENTS.md. Overwrite?', message: 'AGENTS.md', key: 'agentsMd' },
+    claudeCommands: { prompt: 'Found existing .claude/commands/. Overwrite?', message: '.claude/commands/', key: 'claudeCommands' }
+  };
+
+  const config = fileLabels[fileType];
+  if (!config) return;
+
+  // Enhanced: For AGENTS.md, check if it has Forge markers
+  if (fileType === 'agentsMd') {
+    const agentsPath = path.join(projectRoot, 'AGENTS.md');
+    const existingContent = fs.readFileSync(agentsPath, 'utf8');
+    const hasUserMarkers = existingContent.includes('<!-- USER:START');
+    const hasForgeMarkers = existingContent.includes('<!-- FORGE:START');
+
+    if (!hasUserMarkers && !hasForgeMarkers) {
+      // No markers - offer 3 options via helper function
+      await promptForAgentsMdWithoutMarkers(question, skipFiles, agentsPath);
+      return;
+    }
+  }
+
+  // Default behavior: Binary y/n for files with markers or .claude/commands
+  const overwrite = await askYesNo(question, config.prompt, true);
+  if (overwrite) {
+    console.log(`  Will overwrite ${config.message}`);
+  } else {
+    skipFiles[config.key] = true;
+    console.log(`  Keeping existing ${config.message}`);
+  }
+}
+
+/**
+ * Display agent selection options
+ */
+
+
+/**
+ * Display agent selection options
+ */
+function displayAgentOptions(agentKeys) {
+  console.log('STEP 1: Select AI Coding Agents');
+  console.log('================================');
+  console.log('');
+  console.log('Which AI coding agents do you use?');
+  console.log('(Enter numbers separated by spaces, or "all")');
+  console.log('');
+
+  agentKeys.forEach((key, index) => {
+    const agent = AGENTS[key];
+    console.log(`  ${(index + 1).toString().padStart(2)}) ${agent.name.padEnd(20)} - ${agent.description}`);
+  });
+  console.log('');
+  console.log('  all) Install for all agents');
+  console.log('');
+}
+
+/**
+ * Validate and parse agent selection input
+ */
+
+
+/**
+ * Validate and parse agent selection input
+ */
+function validateAgentSelection(input, agentKeys) {
+  // Handle empty input
+  if (!input?.trim()) {
+    return { valid: false, agents: [], message: 'Please enter at least one agent number or "all".' };
+  }
+
+  // Handle "all" selection
+  if (input.toLowerCase() === 'all') {
+    return { valid: true, agents: agentKeys, message: null };
+  }
+
+  // Parse numbers
+  const nums = input.split(/[\s,]+/).map(n => Number.parseInt(n.trim())).filter(n => !Number.isNaN(n));
+
+  // Validate numbers are in range
+  const validNums = nums.filter(n => n >= 1 && n <= agentKeys.length);
+  const invalidNums = nums.filter(n => n < 1 || n > agentKeys.length);
+
+  if (invalidNums.length > 0) {
+    console.log(`  ⚠ Invalid numbers ignored: ${invalidNums.join(', ')} (valid: 1-${agentKeys.length})`);
+  }
+
+  // Deduplicate selected agents using Set
+  const selectedAgents = [...new Set(validNums.map(n => agentKeys[n - 1]))].filter(Boolean);
+
+  if (selectedAgents.length === 0) {
+    return { valid: false, agents: [], message: 'No valid agents selected. Please try again.' };
+  }
+
+  return { valid: true, agents: selectedAgents, message: null };
+}
+
+/**
+ * Prompt for agent selection with validation loop
+ */
+
+
+/**
+ * Prompt for agent selection with validation loop
+ */
+async function promptForAgentSelection(question, agentKeys) {
+  displayAgentOptions(agentKeys);
+
+  let selectedAgents = [];
+
+  // Loop until valid input is provided
+  while (selectedAgents.length === 0) {
+    const answer = await question('Your selection: ');
+    const result = validateAgentSelection(answer, agentKeys);
+
+    if (result.valid) {
+      selectedAgents = result.agents;
+    } else if (result.message) {
+      console.log(`  ${result.message}`);
+    }
+  }
+
+  return selectedAgents;
+}
+
+/**
+ * Attempt semantic merge with fallback to replace
+ * Reduces cognitive complexity by extracting merge logic (S3776)
+ * @param {string} destPath - Destination file path
+ * @param {string} existingContent - Existing file content
+ * @param {string} newContent - New template content
+ * @param {string} srcPath - Source template path
+ */
+
+
+/**
+ * Attempt semantic merge with fallback to replace
+ * Reduces cognitive complexity by extracting merge logic (S3776)
+ * @param {string} destPath - Destination file path
+ * @param {string} existingContent - Existing file content
+ * @param {string} newContent - New template content
+ * @param {string} srcPath - Source template path
+ */
+function trySemanticMerge(destPath, existingContent, newContent, srcPath) {
+  try {
+    // Add markers to enable future marker-based updates
+    const semanticMerged = contextMerge.semanticMerge(existingContent, newContent, {
+      addMarkers: true
+    });
+    fs.writeFileSync(destPath, semanticMerged, 'utf8');
+    console.log('  Updated: AGENTS.md (intelligent merge - preserved your content)');
+    console.log('  Note: Added USER/FORGE markers for future updates');
+  } catch (error) {
+    console.log(`  Warning: Semantic merge failed (${error.message}), using replace strategy`);
+    if (copyFile(srcPath, 'AGENTS.md')) {
+      console.log('  Updated: AGENTS.md (universal standard)');
+    }
+  }
+}
+
+/**
+ * Handle AGENTS.md installation
+ */
+
+
+/**
+ * Handle AGENTS.md installation
+ */
+async function installAgentsMd(skipFiles) {
+  if (skipFiles.agentsMd) {
+    console.log('  Skipped: AGENTS.md (keeping existing)');
+    return;
+  }
+
+  const agentsSrc = path.join(packageDir, 'AGENTS.md');
+  const agentsDest = path.join(projectRoot, 'AGENTS.md');
+
+  // Try smart merge if file exists
+  if (fs.existsSync(agentsDest)) {
+    const existingContent = fs.readFileSync(agentsDest, 'utf8');
+    const newContent = fs.readFileSync(agentsSrc, 'utf8');
+    const merged = smartMergeAgentsMd(existingContent, newContent);
+
+    if (merged) {
+      // Has markers - use existing smart merge
+      fs.writeFileSync(agentsDest, merged, 'utf8');
+      console.log('  Updated: AGENTS.md (preserved USER sections)');
+    } else if (skipFiles.useSemanticMerge) {
+      // Enhanced: No markers but user chose intelligent merge
+      trySemanticMerge(agentsDest, existingContent, newContent, agentsSrc);
+    } else if (copyFile(agentsSrc, 'AGENTS.md')) {
+      // No markers, do normal copy (user already approved overwrite)
+      console.log('  Updated: AGENTS.md (universal standard)');
+    }
+  } else if (copyFile(agentsSrc, 'AGENTS.md')) {
+    // New file
+    console.log('  Created: AGENTS.md (universal standard)');
+
+    // Detect project type and update AGENTS.md
+    const detection = detectProjectType();
+    if (detection.hasPackageJson) {
+      updateAgentsMdWithProjectType(detection);
+      displayProjectType(detection);
+    }
+  }
+}
+
+/**
+ * Load Claude commands for conversion
+ */
+
+
+/**
+ * Load Claude commands for conversion
+ */
+function loadClaudeCommands(selectedAgents) {
+  const claudeCommands = {};
+  const needsClaudeCommands = selectedAgents.includes('claude') ||
+    selectedAgents.some(a => AGENTS[a].needsConversion || AGENTS[a].copyCommands);
+
+  if (!needsClaudeCommands) {
+    return claudeCommands;
+  }
+
+  getWorkflowCommands().forEach(cmd => {
+    const cmdPath = path.join(projectRoot, `.claude/commands/${cmd}.md`);
+    const content = readFile(cmdPath);
+    if (content) {
+      claudeCommands[`${cmd}.md`] = content;
+    }
+  });
+
+  return claudeCommands;
+}
+
+/**
+ * Setup agents with progress indication
+ * Delegates to setupSelectedAgents to avoid duplicate implementations (S4144)
+ */
+
+
+/**
+ * Setup agents with progress indication
+ * Delegates to setupSelectedAgents to avoid duplicate implementations (S4144)
+ */
+async function setupAgentsWithProgress(selectedAgents, claudeCommands, skipFiles) {
+  await setupSelectedAgents(selectedAgents, claudeCommands, skipFiles);
+}
+
+/**
+ * Display final setup summary
+ */
+
+
+/**
+ * Display final setup summary
+ */
+function displaySetupSummary(selectedAgents) {
+  console.log('');
+  console.log('==============================================');
+  console.log(`  Forge v${VERSION} Setup Complete!`);
+  console.log('==============================================');
+  console.log('');
+  console.log('What\'s installed:');
+  console.log('  - AGENTS.md (universal instructions)');
+
+  const workflowCount = getWorkflowCommands().length;
+  selectedAgents.forEach(key => {
+    const agent = AGENTS[key];
+    if (agent.linkFile) {
+      console.log(`  - ${agent.linkFile} (${agent.name})`);
+    }
+    if (agent.hasCommands && key === 'claude') {
+      console.log(`  - .claude/commands/ (${workflowCount} workflow commands)`);
+    } else if (agent.hasCommands && key !== 'codex' && agent.dirs[0]) {
+      console.log(`  - ${agent.dirs[0]}/ (${workflowCount} workflow commands)`);
+    }
+    if (key === 'codex') {
+      const skillCount = listCodexSkillEntries(packageDir).length;
+      console.log(`  - .codex/skills/<stage>/SKILL.md (${skillCount} stage skills)`);
+    } else if (agent.hasSkill) {
+      const skillDir = agent.dirs.find(d => d.includes('/skills/'));
+      if (skillDir) {
+        console.log(`  - ${skillDir}/SKILL.md`);
+      }
+    }
+  });
+
+  console.log('');
+  console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
+  console.log('📋  NEXT STEP - Complete AGENTS.md');
+  console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
+  console.log('');
+  console.log('Ask your AI agent:');
+  console.log('  "Fill in the project description in AGENTS.md"');
+  console.log('');
+  console.log('The agent will:');
+  console.log('  ✓ Add one-sentence project description');
+  console.log('  ✓ Confirm package manager');
+  console.log('  ✓ Verify build commands');
+  console.log('');
+  console.log('Takes ~30 seconds. Done!');
+  console.log('');
+  console.log('💡 As you work: Add project patterns to AGENTS.md');
+  console.log('   USER:START section. Keep it minimal - budget is');
+  console.log('   ~150-200 instructions max.');
+  console.log('');
+  console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
+  console.log('');
+  console.log('Project Tools Status:');
+  console.log('');
+
+  // Beads status
+  if (isBeadsInitialized()) {
+    console.log('  ✓ Beads initialized - Track work: bd ready');
+  } else if (checkForBeads()) {
+    console.log('  ! Beads available - Run: bd init');
+  } else {
+    console.log(`  - Beads not installed - Run: ${PKG_MANAGER} install -g @beads/bd && bd init`);
+  }
+
+  // Skills status
+  if (isSkillsInitialized()) {
+    console.log('  ✓ Skills initialized - Manage skills: skills list');
+  } else if (checkForSkills()) {
+    console.log('  ! Skills available - Run: skills init');
+  } else {
+    console.log(`  - Skills not installed - Run: ${PKG_MANAGER} install -g @forge/skills`);
+  }
+
+  console.log('');
+  console.log('Start with: /status');
+  console.log('');
+  console.log(`Package manager: ${PKG_MANAGER}`);
+  console.log('');
+}
+
+
+// Interactive setup
+// @private - Currently unused, reserved for future interactive flow
+
+
+
+// Interactive setup
+// @private - Currently unused, reserved for future interactive flow
+async function _interactiveSetup() {
+  const rl = readline.createInterface({
+    input: process.stdin,
+    output: process.stdout
+  });
+
+  let setupCompleted = false;
+
+  // Handle Ctrl+C gracefully
+  rl.on('close', () => {
+    if (!setupCompleted) {
+      console.log('\n\nSetup cancelled.');
+      process.exit(0);
+    }
+  });
+
+  // Handle input errors
+  rl.on('error', (err) => {
+    console.error('Input error:', err.message);
+    process.exit(1);
+  });
+
+  const question = (prompt) => new Promise(resolve => rl.question(prompt, resolve));
+
+  showBanner('Agent Configuration');
+
+  // Show target directory
+  console.log(`  Target directory: ${process.cwd()}`);
+  console.log('  (Use --path <dir> to change target directory)');
+  console.log('');
+
+  // Check prerequisites first
+  checkPrerequisites({ requireJq: true });
+  console.log('');
+
+  // =============================================
+  // PROJECT DETECTION
+  // =============================================
+  const projectStatus = await detectProjectStatus();
+  displayInstallationStatus(projectStatus);
+
+  // Track which files to skip based on user choices
+  const skipFiles = {
+    agentsMd: false,
+    claudeCommands: false
+  };
+
+  // Ask about overwriting existing files
+  await promptForFileOverwrite(question, 'agentsMd', projectStatus.hasAgentsMd, skipFiles);
+  await promptForFileOverwrite(question, 'claudeCommands', projectStatus.hasClaudeCommands, skipFiles);
+
+  if (projectStatus.type !== 'fresh') {
+    console.log('');
+  }
+
+  // =============================================
+  // STEP 1: Agent Selection
+  // =============================================
+  const agentKeys = Object.keys(AGENTS);
+  const selectedAgents = await promptForAgentSelection(question, agentKeys);
+
+  console.log('');
+  console.log('Installing Forge workflow...');
+
+  // Install AGENTS.md
+  await installAgentsMd(skipFiles);
+  console.log('');
+
+  // Setup core documentation
+  setupCoreDocs();
+  console.log('');
+
+  // Load Claude commands if needed
+  let claudeCommands = {};
+  if (selectedAgents.includes('claude') || selectedAgents.some(a => AGENTS[a].needsConversion || AGENTS[a].copyCommands)) {
+    // First ensure Claude is set up
+    if (selectedAgents.includes('claude')) {
+      await setupAgent('claude', null, skipFiles);
+    }
+    // Then load the commands
+    claudeCommands = loadClaudeCommands(selectedAgents);
+  }
+
+  // Setup each selected agent with progress indication
+  await setupAgentsWithProgress(selectedAgents, claudeCommands, skipFiles);
+
+  // =============================================
+  // STEP 2: Project Tools Setup
+  // =============================================
+  await setupProjectTools(rl, question);
+
+  // =============================================
+  // STEP 3: External Services Configuration
+  // =============================================
+  console.log('');
+  console.log('STEP 3: External Services (Optional)');
+  console.log('=====================================');
+
+  await configureExternalServices(rl, question, selectedAgents, projectStatus);
+
+  setupCompleted = true;
+  rl.close();
+
+  // =============================================
+  // Final Summary
+  // =============================================
+  displaySetupSummary(selectedAgents);
+}
+
+// Parse CLI flags
+
+
+// Detect Husky and offer migration to Lefthook
+// Called before installGitHooks() in setup flows
+async function handleHuskyMigration() {
+  const detection = detectHusky(projectRoot);
+  if (!detection.found) return;
+
+  console.log('Husky detected — migrating to Lefthook...');
+
+  // In interactive mode, ask the user before proceeding
+  if (!NON_INTERACTIVE) {
+    const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
+    const question = (prompt) => new Promise(resolve => rl.question(prompt, resolve));
+    const userApproved = await askYesNo(question, 'Migrate Husky hooks to Lefthook?', false);
+    rl.close();
+    if (!userApproved) {
+      console.log('  Skipped Husky migration (user declined)');
+      console.log('');
+      return;
+    }
+  }
+
+  const result = migrateHusky(projectRoot, { nonInteractive: true });
+
+  if (result.success) {
+    console.log(`  Migrated ${result.mappedCount} hook(s) to lefthook.yml`);
+    if (result.unmappedCount > 0) {
+      console.warn(`  ${result.unmappedCount} hook(s) could not be auto-mapped:`);
+      for (const w of result.warnings) {
+        console.warn(`    - ${w}`);
+      }
+    }
+    if (result.hooksPathUnset) {
+      console.log('  Unset core.hooksPath git config');
+    }
+    console.log('  Removed .husky/ directory');
+    console.log('');
+  } else {
+    // Validation failed (e.g. symlink detected)
+    for (const w of result.warnings) {
+      console.warn(`  ${w}`);
+    }
+    console.log('');
+  }
+}
+
+// Install git hooks via lefthook
+// SECURITY: Uses execSync with HARDCODED strings only (no user input)
+
+
+// Install git hooks via lefthook
+// SECURITY: Uses execSync with HARDCODED strings only (no user input)
+function installGitHooks() { // NOSONAR — Extracted as-is from bin/forge.js; complexity reduction deferred
+  console.log('Installing git hooks (TDD enforcement)...');
+
+  // Skip lefthook.yml creation if binary is not available
+  const lefthookStatus = checkLefthookStatus(projectRoot);
+  if (!lefthookStatus.binaryAvailable) {
+    if (lefthookStatus.message) {
+      console.warn(`  \u26A0 Skipping lefthook setup: ${lefthookStatus.message}`);
+    } else {
+      console.warn('  \u26A0 Skipping lefthook setup: binary not available');
+    }
+    return;
+  }
+
+  // Check if lefthook.yml exists (it should, as it's in the package)
+  const lefthookConfig = path.join(packageDir, 'lefthook.yml');
+  const targetHooks = path.join(projectRoot, '.forge/hooks');
+
+  try {
+    // Copy lefthook.yml to project root
+    const lefthookTarget = path.join(projectRoot, 'lefthook.yml');
+    if (!fs.existsSync(lefthookTarget)) {
+      if (copyFile(lefthookConfig, 'lefthook.yml')) {
+        console.log('  ✓ Created lefthook.yml');
+      }
+    }
+
+    // Copy check-tdd.js hook script
+    const hookSource = path.join(packageDir, '.forge/hooks/check-tdd.js');
+    if (fs.existsSync(hookSource)) {
+      // Ensure .forge/hooks directory exists
+      if (!fs.existsSync(targetHooks)) {
+        fs.mkdirSync(targetHooks, { recursive: true });
+      }
+
+      const hookTarget = path.join(targetHooks, 'check-tdd.js');
+      if (copyFile(hookSource, hookTarget)) {
+        console.log('  ✓ Created .forge/hooks/check-tdd.js');
+
+        // Make hook executable (Unix systems)
+        try {
+          fs.chmodSync(hookTarget, 0o755); // NOSONAR — 755 is intentional: git hooks must be executable
+        } catch (err) {
+          // Windows doesn't need chmod
+          console.warn('chmod not available (Windows):', err.message);
+        }
+      }
+    }
+
+    // Try to install lefthook hooks
+    // SECURITY: Using execFileSync with hardcoded commands (no user input)
+    try {
+      // Try npx first (local install), fallback to global
+      try {
+        secureExecFileSync('npx', ['lefthook', 'install'], { stdio: 'inherit', cwd: projectRoot });
+        console.log('  ✓ Lefthook hooks installed (local)');
+      } catch (error_) {
+        // Fallback to global lefthook
+        console.warn('npx lefthook failed, trying global:', error_.message);
+        execFileSync('lefthook', ['version'], { stdio: 'ignore' });
+        execFileSync('lefthook', ['install'], { stdio: 'inherit', cwd: projectRoot });
+        console.log('  ✓ Lefthook hooks installed (global)');
+      }
+    } catch (err) {
+      console.warn('Lefthook installation failed:', err.message);
+      console.log('  ℹ Lefthook not found. Install it:');
+      console.log('    bun add -d lefthook  (recommended)');
+      console.log('    OR: bun add -g lefthook  (global)');
+      console.log('    Then run: bunx lefthook install');
+    }
+
+    console.log('');
+
+  } catch (error) {
+    console.log('  ⚠ Failed to install hooks:', error.message);
+    console.log('  You can install manually later with: lefthook install');
+    console.log('');
+  }
+}
+
+// Check if lefthook is already installed in project (delegates to lib/lefthook-check)
+
+
+// Check if lefthook is already installed in project (delegates to lib/lefthook-check)
+function checkForLefthook() {
+  const status = checkLefthookStatus(projectRoot);
+  if (status.installed && !status.binaryAvailable) {
+    console.warn(`  \u26A0 ${status.message}`);
+  }
+  return status;
+}
+
+function repairDeclaredLefthookDependency(selectedAgents) {
+  if (!needsWorkflowRuntimeAssets(selectedAgents)) {
+    return { attempted: false, repaired: false, reason: 'workflow-hooks-not-required' };
+  }
+
+  const status = checkLefthookStatus(projectRoot);
+  if (!status.installed || status.binaryAvailable) {
+    return {
+      attempted: false,
+      repaired: false,
+      reason: status.binaryAvailable ? 'binary-present' : 'dependency-not-declared'
+    };
+  }
+
+  console.log('Installing lefthook dependencies (binary missing)...');
+  try {
+    secureExecFileSync(PKG_MANAGER, ['install'], { stdio: 'inherit', cwd: projectRoot });
+    console.log('  ✓ Lefthook binary restored');
+    console.log('');
+    return { attempted: true, repaired: true };
+  } catch (err) {
+    console.warn('Lefthook install failed:', err.message);
+    console.log(`  ⚠ ${status.message}`);
+    console.log('');
+    return { attempted: true, repaired: false, error: err };
+  }
+}
+
+// Check if Beads is installed (global, local, or bunx-capable)
+
+
+// Check if Beads is installed (global, local, or bunx-capable)
+function checkForBeads() {
+  // Try global install first
+  try {
+    secureExecFileSync('bd', ['version'], { stdio: 'ignore' });
+    return 'global';
+  } catch (err) {
+    // Not global
+    console.warn('Beads not found globally:', err.message);
+  }
+
+  // Check if bunx can run it
+  try {
+    secureExecFileSync('bunx', ['@beads/bd', 'version'], { stdio: 'ignore' });
+    return 'bunx';
+  } catch (err) {
+    // Not bunx-capable
+    console.warn('Beads not available via bunx:', err.message);
+  }
+
+  // Check local project installation
+  const pkgPath = path.join(projectRoot, 'package.json');
+  if (!fs.existsSync(pkgPath)) return null;
+
+  try {
+    const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf8'));
+    const isInstalled = pkg.devDependencies?.['@beads/bd'] || pkg.dependencies?.['@beads/bd'];
+    return isInstalled ? 'local' : null;
+  } catch (err) {
+    console.warn('Failed to check Beads in package.json:', err.message);
+    return null;
+  }
+}
+// Check if Beads is initialized in project — delegates to lib/beads-setup
+
+// Check if Beads is initialized in project — delegates to lib/beads-setup
+function isBeadsInitialized() {
+  return beadsSetupLib.isBeadsInitialized(projectRoot);
+}
+
+// Initialize Beads in the project using the defensive safeBeadsInit wrapper
+// Handles config/gitignore writes, hook snapshot/restore, and JSONL pre-seeding
+
+
+// Initialize Beads in the project using the defensive safeBeadsInit wrapper
+// Handles config/gitignore writes, hook snapshot/restore, and JSONL pre-seeding
+function initializeBeads(installType) {
+  console.log('Initializing Beads in project...');
+
+  // Build the execBdInit function based on installType
+  const execBdInit = (root) => {
+    // SECURITY: execFileSync with hardcoded commands
+    if (installType === 'global') {
+      secureExecFileSync('bd', ['init'], { stdio: 'inherit', cwd: root });
+    } else if (installType === 'bunx') {
+      secureExecFileSync('bunx', ['@beads/bd', 'init'], { stdio: 'inherit', cwd: root });
+    } else if (installType === 'local') {
+      secureExecFileSync('npx', ['bd', 'init'], { stdio: 'inherit', cwd: root });
+    }
+  };
+
+  // Derive prefix from package.json name or directory name
+  let prefix;
+  try {
+    const pkg = JSON.parse(fs.readFileSync(path.join(projectRoot, 'package.json'), 'utf8'));
+    prefix = pkg.name || path.basename(projectRoot);
+  } catch (_e) { // NOSONAR — fallback to directory name if package.json unreadable
+    prefix = path.basename(projectRoot);
+  }
+
+  try {
+    const result = beadsSetupLib.safeBeadsInit(projectRoot, {
+      prefix,
+      execBdInit,
+      restoreLefthook: (root) => {
+        try {
+          secureExecFileSync('lefthook', ['install'], { stdio: 'ignore', cwd: root });
+        } catch (_e) { // NOSONAR — lefthook may not be installed yet, non-fatal
+          // lefthook may not be installed yet — non-fatal
+        }
+      }
+    });
+
+    if (result.skipped) {
+      console.log('  ✓ Beads already initialized');
+      return true;
+    }
+
+    if (!result.success) {
+      for (const e of result.errors) {
+        console.log(`  ⚠ ${e}`);
+      }
+      console.log('  Run manually: bd init');
+      return false;
+    }
+
+    for (const w of result.warnings) {
+      console.warn(`  ⚠ ${w}`);
+    }
+    console.log('  ✓ Beads initialized');
+
+    // Run post-init health check (non-fatal)
+    try {
+      const health = beadsHealthCheck(projectRoot);
+      if (health.healthy) {
+        console.log('  ✓ Beads health check passed');
+      } else {
+        console.log(`  ⚠ Beads health check failed at ${health.failedStep}: ${health.error}`);
+      }
+    } catch (_healthErr) { // NOSONAR — health check is best-effort, non-fatal
+      // Health check is best-effort — don't block setup
+    }
+
+    return true;
+  } catch (err) {
+    console.log('  ⚠ Failed to initialize Beads:', err.message);
+    console.log('  Run manually: bd init');
+    return false;
+  }
+}
+
+// Check if Skills CLI is installed
+
+
+// Check if Skills CLI is installed
+function checkForSkills() {
+  // Try global install first
+  try {
+    secureExecFileSync('skills', ['--version'], { stdio: 'ignore' });
+    return 'global';
+  } catch (_err) { // NOSONAR - S2486: Expected when Skills is not installed globally
+  }
+
+  // Check if bunx can run it
+  try {
+    secureExecFileSync('bunx', ['@forge/skills', '--version'], { stdio: 'ignore' });
+    return 'bunx';
+  } catch (_err) { // NOSONAR - S2486: Expected when Skills is not available via bunx
+  }
+
+  // Check local project installation
+  const pkgPath = path.join(projectRoot, 'package.json');
+  if (!fs.existsSync(pkgPath)) return null;
+
+  try {
+    const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf8'));
+    const isInstalled = pkg.devDependencies?.['@forge/skills'] || pkg.dependencies?.['@forge/skills'];
+    return isInstalled ? 'local' : null;
+  } catch (_err) { // NOSONAR - S2486: Returns null on malformed package.json
+    return null;
+  }
+}
+
+// Check if Skills is initialized in project
+
+
+// Check if Skills is initialized in project
+function isSkillsInitialized() {
+  return fs.existsSync(path.join(projectRoot, '.skills'));
+}
+
+// Initialize Skills in the project
+
+
+// Initialize Skills in the project
+function initializeSkills(installType) {
+  console.log('Initializing Skills in project...');
+
+  try {
+    // Using secureExecFileSync to validate PATH and mitigate S4036
+    if (installType === 'global') {
+      secureExecFileSync('skills', ['init'], { stdio: 'inherit', cwd: projectRoot });
+    } else if (installType === 'bunx') {
+      secureExecFileSync('bunx', ['@forge/skills', 'init'], { stdio: 'inherit', cwd: projectRoot });
+    } else if (installType === 'local') {
+      secureExecFileSync('npx', ['skills', 'init'], { stdio: 'inherit', cwd: projectRoot });
+    }
+    console.log('  ✓ Skills initialized');
+    return true;
+  } catch (err) {
+    console.log('  ⚠ Failed to initialize Skills:', err.message);
+    console.log('  Run manually: skills init');
+    return false;
+  }
+}
+
+// Prompt for Beads setup - extracted to reduce cognitive complexity
+
+
+// Prompt for Beads setup - extracted to reduce cognitive complexity
+async function promptBeadsSetup(question) {
+  console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
+  console.log('Beads Setup (Recommended)');
+  console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
+  console.log('');
+
+  const beadsInitialized = isBeadsInitialized();
+  const beadsStatus = checkForBeads();
+
+  if (beadsInitialized) {
+    console.log('✓ Beads is already initialized in this project');
+    console.log('');
+    return;
+  }
+
+  if (beadsStatus) {
+    // Already installed, just need to initialize
+    console.log(`ℹ Beads is installed (${beadsStatus}), but not initialized`);
+    const initBeads = await question('Initialize Beads in this project? (y/n): ');
+
+    if (initBeads.toLowerCase() === 'y') {
+      initializeBeads(beadsStatus);
+    } else {
+      console.log('Skipped Beads initialization. Run manually: bd init');
+    }
+    console.log('');
+    return;
+  }
+
+  // Not installed
+  console.log('ℹ Beads is not installed');
+  const installBeads = await question('Install Beads? (y/n): ');
+
+  if (installBeads.toLowerCase() !== 'y') {
+    console.log('Skipped Beads installation');
+    console.log('');
+    return;
+  }
+
+  console.log('');
+  console.log('Choose installation method:');
+  console.log('  1. Global (recommended) - Available system-wide');
+  console.log('  2. Local - Project-specific devDependency');
+  console.log('  3. Bunx - Use via bunx (requires bun)');
+  console.log('');
+  const method = await question('Choose method (1-3): ');
+
+  console.log('');
+  installBeadsWithMethod(method);
+  console.log('');
+}
+
+// Helper: Install tool via bunx - extracted to reduce cognitive complexity
+
+
+// Helper: Install tool via bunx - extracted to reduce cognitive complexity
+function installViaBunx(packageName, versionArgs, initFn, toolName) {
+  console.log('Testing bunx capability...');
+  try {
+    secureExecFileSync('bunx', [packageName, ...versionArgs], { stdio: 'ignore' });
+    console.log('  ✓ Bunx is available');
+    initFn('bunx');
+  } catch (err) {
+    console.warn(`${toolName} bunx test failed:`, err.message);
+    console.log('  ⚠ Bunx not available. Install bun first: curl -fsSL https://bun.sh/install | bash');
+  }
+}
+
+// Helper: Install Beads with chosen method - extracted to reduce cognitive complexity
+// SECURITY NOTE: Downloads and executes a remote PowerShell script.
+// The npm @beads/bd package is broken on Windows (GitHub Issue #1031, closed "not planned"),
+// so the official PowerShell installer is the only supported path.
+// Mitigations: HTTPS transport (prevents MITM), official beads repo, user-visible URL.
+// Follow-up: pin to a versioned release tag once beads publishes tagged releases (for example v0.49.1).
+const BEADS_INSTALL_PS1_URL = 'https://raw.githubusercontent.com/steveyegge/beads/main/install.ps1';
+
+
+
+function installBeadsOnWindows() {
+  console.log('  (Windows detected: using PowerShell installer)');
+  console.log(`  Downloading: ${BEADS_INSTALL_PS1_URL}`);
+  secureExecFileSync('powershell.exe', [
+    '-NoProfile', '-NonInteractive', '-Command',
+    `irm ${BEADS_INSTALL_PS1_URL} | iex`
+  ], { stdio: 'inherit' });
+}
+
+
+
+function installBeadsWithMethod(method) { // NOSONAR — Extracted as-is from bin/forge.js; complexity reduction deferred
+  try {
+    // SECURITY: secureExecFileSync with hardcoded commands
+    if (method === '1') {
+      console.log('Installing Beads globally...');
+      if (process.platform === 'win32') {
+        installBeadsOnWindows();
+      } else {
+        const pkgManager = PKG_MANAGER === 'bun' ? 'bun' : 'npm';
+        secureExecFileSync(pkgManager, ['install', '-g', '@beads/bd'], { stdio: 'inherit' });
+      }
+      console.log('  ✓ Beads installed globally');
+      initializeBeads('global');
+    } else if (method === '2') {
+      console.log('Installing Beads locally...');
+      // On Windows, npm postinstall for @beads/bd runs Expand-Archive which has EPERM file-locking
+      // (GitHub Issue #1031, closed "not planned") — same root cause as global install.
+      // Redirect Windows users to the global PowerShell installer instead.
+      if (process.platform === 'win32') {
+        console.log('  ⚠ Local install not supported on Windows (npm @beads/bd EPERM issue).');
+        console.log('  Falling back to global PowerShell installer...');
+        installBeadsOnWindows();
+      } else {
+        const pkgManager = PKG_MANAGER === 'bun' ? 'bun' : 'npm';
+        secureExecFileSync(pkgManager, ['install', '-D', '@beads/bd'], { stdio: 'inherit', cwd: projectRoot });
+      }
+      console.log('  ✓ Beads installed');
+      // On Windows the fallback was global (PowerShell installer), so init as 'global'
+      initializeBeads(process.platform === 'win32' ? 'global' : 'local');
+    } else if (method === '3') {
+      installViaBunx('@beads/bd', ['version'], initializeBeads, 'Beads');
+    } else {
+      console.log('Invalid choice. Skipping Beads installation.');
+    }
+  } catch (err) {
+    console.warn('Beads installation failed:', err.message);
+    console.log('  ⚠ Failed to install Beads:', err.message);
+    if (process.platform === 'win32') {
+      console.log(`  Run manually: irm ${BEADS_INSTALL_PS1_URL} | iex`);
+    } else {
+      console.log(`  Run manually: ${PKG_MANAGER === 'bun' ? 'bun add -g' : 'npm install -g'} @beads/bd && bd init`);
+    }
+  }
+}
+
+// Helper: Get package-manager-specific install args for Skills
+
+
+// Helper: Get package-manager-specific install args for Skills
+function getSkillsInstallArgs(scope) {
+  const globalFlag = scope === 'global' ? '-g' : '-D';
+  if (PKG_MANAGER === 'yarn' && scope === 'global') {
+    return ['global', 'add', '@forge/skills'];
+  }
+  const cmd = (PKG_MANAGER === 'bun' || PKG_MANAGER === 'pnpm') ? 'add' : 'install';
+  return [cmd, globalFlag, '@forge/skills'];
+}
+
+// Helper: Install Skills with chosen method - extracted to reduce cognitive complexity
+
+
+// Helper: Install Skills with chosen method - extracted to reduce cognitive complexity
+function installSkillsWithMethod(method) {
+  try {
+    if (method === '1') {
+      console.log('Installing Skills globally...');
+      secureExecFileSync(PKG_MANAGER, getSkillsInstallArgs('global'), { stdio: 'inherit' });
+      console.log('  ✓ Skills installed globally');
+      initializeSkills('global');
+    } else if (method === '2') {
+      console.log('Installing Skills locally...');
+      secureExecFileSync(PKG_MANAGER, getSkillsInstallArgs('local'), { stdio: 'inherit', cwd: projectRoot });
+      console.log('  ✓ Skills installed locally');
+      initializeSkills('local');
+    } else if (method === '3') {
+      installViaBunx('@forge/skills', ['--version'], initializeSkills, 'Skills');
+    } else {
+      console.log('Invalid choice. Skipping Skills installation.');
+    }
+  } catch (err) {
+    console.warn('Skills installation failed:', err.message);
+    console.log('  ⚠ Failed to install Skills:', err.message);
+    console.log(`  Run manually: ${PKG_MANAGER === 'bun' ? 'bun add -g' : 'npm install -g'} @forge/skills && skills init`);
+  }
+}
+
+// Prompt for Skills setup - extracted to reduce cognitive complexity
+
+
+// Prompt for Skills setup - extracted to reduce cognitive complexity
+async function promptSkillsSetup(question) {
+  console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
+  console.log('Skills CLI Setup (Recommended)');
+  console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
+  console.log('');
+
+  const skillsInitialized = isSkillsInitialized();
+  const skillsStatus = checkForSkills();
+
+  if (skillsInitialized) {
+    console.log('✓ Skills is already initialized in this project');
+    console.log('');
+    return;
+  }
+
+  if (skillsStatus) {
+    // Already installed, just need to initialize
+    console.log(`ℹ Skills is installed (${skillsStatus}), but not initialized`);
+    const initSkills = await question('Initialize Skills in this project? (y/n): ');
+
+    if (initSkills.toLowerCase() === 'y') {
+      initializeSkills(skillsStatus);
+    } else {
+      console.log('Skipped Skills initialization. Run manually: skills init');
+    }
+    console.log('');
+    return;
+  }
+
+  // Not installed
+  console.log('ℹ Skills is not installed');
+  const installSkills = await question('Install Skills CLI? (y/n): ');
+
+  if (installSkills.toLowerCase() !== 'y') {
+    console.log('Skipped Skills installation');
+    console.log('');
+    return;
+  }
+
+  console.log('');
+  console.log('Choose installation method:');
+  console.log('  1. Global (recommended) - Available system-wide');
+  console.log('  2. Local - Project-specific devDependency');
+  console.log('  3. Bunx - Use via bunx (requires bun)');
+  console.log('');
+  const installMethod = await question('Choose installation method (1-3): ');
+
+  console.log('');
+  installSkillsWithMethod(installMethod);
+  console.log('');
+}
+
+// Interactive setup for Beads and Skills
+
+
+// Interactive setup for Beads and Skills
+async function setupProjectTools(rl, question) {
+  console.log('');
+  console.log('═══════════════════════════════════════════════════════════');
+  console.log('  STEP 2: Project Tools (Recommended)');
+  console.log('═══════════════════════════════════════════════════════════');
+  console.log('');
+  console.log('Forge recommends three tools for enhanced workflows:');
+  console.log('');
+  console.log('• Beads - Git-backed issue tracking');
+  console.log('  Persists tasks across sessions, tracks dependencies.');
+  console.log('  Command: bd ready, bd create, bd close');
+  console.log('');
+  console.log('• Skills - Universal SKILL.md management');
+  console.log('  Manage AI agent skills across all agents.');
+  console.log('  Command: skills create, skills list, skills sync');
+  console.log('');
+
+  // Use helper functions to reduce complexity
+  await promptBeadsSetup(question);
+  await promptSkillsSetup(question);
+}
+
+// Auto-setup Beads in quick mode - extracted to reduce cognitive complexity
+
+
+// Auto-setup Beads in quick mode - extracted to reduce cognitive complexity
+function autoSetupBeadsInQuickMode() { // NOSONAR — Extracted as-is from bin/forge.js; complexity reduction deferred
+  const beadsStatus = checkForBeads();
+  const beadsInitialized = isBeadsInitialized();
+
+  if (!beadsInitialized && beadsStatus) {
+    console.log('📦 Initializing Beads...');
+    initializeBeads(beadsStatus);
+    console.log('');
+  } else if (!beadsInitialized && !beadsStatus) {
+    console.log('📦 Installing Beads globally...');
+    try {
+      // SECURITY: use PowerShell on Windows (npm @beads/bd is broken on Windows - Issue #1031)
+      if (process.platform === 'win32') {
+        installBeadsOnWindows();
+      } else {
+        const pkgManager = PKG_MANAGER === 'bun' ? 'bun' : 'npm';
+        secureExecFileSync(pkgManager, ['install', '-g', '@beads/bd'], { stdio: 'inherit' });
+      }
+      console.log('  ✓ Beads installed globally');
+      initializeBeads('global');
+    } catch (err) {
+      // Installation failed - provide manual instructions
+      console.log('  ⚠ Could not install Beads automatically');
+      console.log(`    Error: ${err.message}`);
+      if (process.platform === 'win32') {
+        console.log(`  Run manually: irm ${BEADS_INSTALL_PS1_URL} | iex`);
+      } else {
+        console.log(`  Run manually: ${PKG_MANAGER === 'bun' ? 'bun add -g' : 'npm install -g'} @beads/bd && bd init`);
+      }
+    }
+    console.log('');
+  }
+}
+
+// Helper: Auto-install lefthook if not present - extracted to reduce cognitive complexity
+
+
+// Helper: Auto-install lefthook if not present - extracted to reduce cognitive complexity
+function getLefthookInstallArgs(packageManager) {
+  if (packageManager === 'yarn') {
+    return ['add', '--dev', 'lefthook'];
+  }
+  if (packageManager === 'npm') {
+    return ['install', '--save-dev', 'lefthook'];
+  }
+  if (packageManager === 'pnpm') {
+    return ['add', '-D', 'lefthook'];
+  }
+  return ['add', '-d', 'lefthook'];
+}
+
+function getLefthookManualInstallCommand(packageManager) {
+  return `${packageManager} ${getLefthookInstallArgs(packageManager).join(' ')}`;
+}
+
+function autoInstallLefthook() { // NOSONAR — Extracted as-is from bin/forge.js; complexity reduction deferred
+  const status = checkForLefthook();
+
+  // Binary available — nothing to do
+  if (status.binaryAvailable) return;
+
+  // In package.json but binary missing — just need install, not add
+  if (status.installed && !status.binaryAvailable) {
+    console.log('📦 Installing lefthook dependencies (binary missing)...');
+    try {
+      secureExecFileSync(PKG_MANAGER, ['install'], { stdio: 'inherit', cwd: projectRoot });
+      console.log('  ✓ Lefthook binary restored');
+    } catch (err) {
+      console.warn('Lefthook install failed:', err.message);
+      console.log(`  ⚠ ${status.message}`);
+    }
+    console.log('');
+    return;
+  }
+
+  // Not in package.json at all — full install
+  console.log('📦 Installing lefthook for git hooks...');
+  try {
+    // SECURITY: secureExecFileSync with PKG_MANAGER — cross-platform support
+    const installArgs = getLefthookInstallArgs(PKG_MANAGER);
+    secureExecFileSync(PKG_MANAGER, installArgs, { stdio: 'inherit', cwd: projectRoot });
+    console.log('  ✓ Lefthook installed');
+  } catch (err) {
+    console.warn('Lefthook auto-install failed:', err.message);
+    console.log('  ⚠ Could not install lefthook automatically');
+    console.log(`  Run manually: ${getLefthookManualInstallCommand(PKG_MANAGER)}`);
+  }
+  console.log('');
+}
+
+// Helper: Verify a tool is callable after install - extracted to reduce cognitive complexity
+
+
+// Helper: Verify a tool is callable after install - extracted to reduce cognitive complexity
+function verifyToolInstall(command, args, toolName) {
+  try {
+    secureExecFileSync(command, args, { stdio: 'ignore' });
+    return true;
+  } catch (_err) { // NOSONAR - S2486: Intentionally ignored; verification failure is handled by caller
+    console.log(`  ⚠ ${toolName} installed but not callable. Check your PATH.`);
+    return false;
+  }
+}
+
+// Helper: Auto-setup tools (Skills) in quick mode - extracted to reduce cognitive complexity
+
+
+// Helper: Auto-setup tools (Skills) in quick mode - extracted to reduce cognitive complexity
+function autoSetupToolsInQuickMode() {
+  // Beads: auto-install or initialize
+  autoSetupBeadsInQuickMode();
+
+  // Post-install verification for Beads
+  if (isBeadsInitialized()) {
+    verifyToolInstall('bd', ['version'], 'Beads');
+  }
+
+  // Skills: only initialize if already installed (recommended tool)
+  const skillsStatus = checkForSkills();
+  if (skillsStatus && !isSkillsInitialized()) {
+    console.log('📦 Initializing Skills...');
+    initializeSkills(skillsStatus);
+    console.log('');
+  } else if (!skillsStatus) {
+    const installCmd = PKG_MANAGER === 'bun' ? 'bun add -g' : 'npm install -g';
+    console.log(`  ℹ Skills not found — install with: ${installCmd} @forge/skills`);
+    console.log('');
+  }
+}
+
+// Helper: Configure default external services in quick mode - extracted to reduce cognitive complexity
+
+
+// Helper: Configure default external services in quick mode - extracted to reduce cognitive complexity
+function configureDefaultExternalServices(skipExternal) {
+  if (skipExternal) {
+    console.log('');
+    console.log('Skipping external services configuration...');
+    return;
+  }
+
+  console.log('');
+  console.log('Configuring default services...');
+  console.log('');
+
+  const tokens = {
+    CODE_REVIEW_TOOL: 'github-code-quality',
+    CODE_QUALITY_TOOL: 'eslint',
+    PKG_MANAGER: PKG_MANAGER
+  };
+
+  writeEnvTokens(tokens);
+
+  console.log('  * Code Review: GitHub Code Quality (FREE)');
+  console.log('  * Code Quality: ESLint (built-in)');
+  console.log('');
+  console.log('Configuration saved to .env.local');
+}
+
+// Quick setup with defaults
+
+
+// Quick setup with defaults
+async function quickSetup(selectedAgents, skipExternal) {
+  showBanner('Quick Setup');
+  console.log('');
+  console.log('Quick mode: Using defaults...');
+  console.log('');
+
+  // Check prerequisites
+  checkPrerequisites({
+    requireBeadsCli: true,
+    requireGithubCli: true,
+    requireJq: true,
+  });
+  console.log('');
+
+  // Copy AGENTS.md (actionLog tracks it via copyFile)
+  const agentsSrc = path.join(packageDir, 'AGENTS.md');
+  copyFile(agentsSrc, 'AGENTS.md');
+  console.log('');
+
+  // Setup core documentation
+  setupCoreDocs();
+  console.log('');
+
+  ensureWorkflowShellPolicy(selectedAgents);
+
+  // Auto-install lefthook if missing
+  autoInstallLefthook();
+
+  // Auto-setup project tools (Beads, Skills)
+  autoSetupToolsInQuickMode();
+
+  // Load canonical commands and setup agents (reuse existing helpers)
+  const claudeCommands = await loadAndSetupCanonicalCommands(selectedAgents);
+  await setupSelectedAgents(selectedAgents, claudeCommands);
+  ensureWorkflowRuntimeAssets(selectedAgents);
+
+  // Detect Husky and migrate before installing Lefthook hooks
+  await handleHuskyMigration();
+
+  // Install git hooks for TDD enforcement
+  console.log('');
+  installGitHooks();
+
+  // Configure external services with defaults (unless skipped)
+  configureDefaultExternalServices(skipExternal);
+
+  // --sync flag: scaffold Beads GitHub sync workflows without prompting
+  if (SYNC_ENABLED) {
+    await handleSyncScaffold();
+  }
+
+  // Progressive setup summary
+  console.log('');
+  console.log(renderSetupSummary(actionLog, selectedAgents, VERBOSE_MODE));
+  console.log('');
+}
+
+// Helper: Apply merge strategy to existing AGENTS.md - extracted to reduce cognitive complexity
+
+
+// Helper: Apply merge strategy to existing AGENTS.md - extracted to reduce cognitive complexity
+function applyAgentsMdMergeStrategy(mergeStrategy, agentsSrc, agentsDest, existingContent, newContent) {
+  if (mergeStrategy === 'preserve') {
+    console.log('  Preserved: AGENTS.md (--merge=preserve)');
+    return;
+  }
+
+  if (mergeStrategy === 'replace') {
+    if (copyFile(agentsSrc, 'AGENTS.md')) {
+      console.log('  Replaced: AGENTS.md (--merge=replace)');
+    }
+    return;
+  }
+
+  // Default: smart merge
+  const merged = smartMergeAgentsMd(existingContent, newContent);
+  if (merged) {
+    fs.writeFileSync(agentsDest, merged, 'utf8');
+    console.log('  Updated: AGENTS.md (smart merge, preserved USER sections)');
+  } else if (copyFile(agentsSrc, 'AGENTS.md')) {
+    console.log('  Updated: AGENTS.md (universal standard)');
+  }
+}
+
+// Setup AGENTS.md file with merge strategy - extracted to reduce cognitive complexity
+
+
+// Setup AGENTS.md file with merge strategy - extracted to reduce cognitive complexity
+function setupAgentsMdFile(flags, skipFiles) {
+  if (skipFiles.agentsMd) {
+    console.log('  Skipped: AGENTS.md (keeping existing)');
+    return;
+  }
+
+  const agentsSrc = path.join(packageDir, 'AGENTS.md');
+  const agentsDest = path.join(projectRoot, 'AGENTS.md');
+  const mergeStrategy = flags.merge || 'smart';
+
+  if (fs.existsSync(agentsDest)) {
+    const existingContent = fs.readFileSync(agentsDest, 'utf8');
+    const newContent = fs.readFileSync(agentsSrc, 'utf8');
+    applyAgentsMdMergeStrategy(mergeStrategy, agentsSrc, agentsDest, existingContent, newContent);
+  } else if (copyFile(agentsSrc, 'AGENTS.md')) {
+    console.log('  Created: AGENTS.md (universal standard)');
+    const detection = detectProjectType();
+    if (detection.hasPackageJson) {
+      updateAgentsMdWithProjectType(detection);
+      displayProjectType(detection);
+    }
+  }
+}
+
+// Helper: Handle user-provided flags override - extracted to reduce cognitive complexity
+
+
+// Helper: Handle user-provided flags override - extracted to reduce cognitive complexity
+function handleFlagsOverride(flags, projectStatus) {
+  if (!flags.type && !flags.interview) {
+    return;
+  }
+
+  console.log('User-provided flags:');
+  if (flags.type) {
+    console.log(`  --type=${flags.type} (workflow profile override)`);
+    saveWorkflowTypeOverride(flags.type, projectStatus.autoDetected);
+  }
+  if (flags.interview) {
+    console.log('  --interview (context interview mode)');
+    console.log('  Note: Enhanced context gathering is a future feature');
+  }
+  console.log('');
+}
+
+// Helper: Save workflow type override to context - extracted to reduce cognitive complexity
+
+
+// Helper: Save workflow type override to context - extracted to reduce cognitive complexity
+function saveWorkflowTypeOverride(type, autoDetected) {
+  if (!autoDetected) {
+    return;
+  }
+  try {
+    const contextPath = path.join(projectRoot, '.forge', 'context.json');
+    if (fs.existsSync(contextPath)) {
+      const contextData = JSON.parse(fs.readFileSync(contextPath, 'utf8'));
+      contextData.user_provided = contextData.user_provided || {};
+      contextData.user_provided.workflowType = type;
+      contextData.last_updated = new Date().toISOString();
+      fs.writeFileSync(contextPath, JSON.stringify(contextData, null, 2), 'utf8');
+    }
+  } catch (error) {
+    console.warn('  Warning: Could not save workflow type override:', error.message);
+  }
+}
+
+// Helper: Display existing installation status - extracted to reduce cognitive complexity
+
+
+// Helper: Display existing installation status - extracted to reduce cognitive complexity
+function displayExistingInstallation(projectStatus) {
+  if (projectStatus.type === 'fresh') {
+    return;
+  }
+
+  console.log('==============================================');
+  console.log('  Existing Installation Detected');
+  console.log('==============================================');
+  console.log('');
+
+  console.log(projectStatus.type === 'upgrade'
+    ? 'Found existing Forge installation:'
+    : 'Found partial installation:');
+
+  if (projectStatus.hasAgentsMd) console.log('  - AGENTS.md');
+  if (projectStatus.hasClaudeCommands) console.log('  - .claude/commands/');
+  if (projectStatus.hasEnvLocal) console.log('  - .env.local');
+  console.log('');
+}
+
+// Helper: Prompt for overwrite decisions - extracted to reduce cognitive complexity
+
+
+// Helper: Prompt for overwrite decisions - extracted to reduce cognitive complexity
+async function promptForOverwriteDecisions(question, projectStatus, flags = {}) {
+  const skipFiles = {
+    agentsMd: false,
+    claudeCommands: false
+  };
+
+  if (flags.keep) {
+    if (projectStatus.hasAgentsMd) {
+      skipFiles.agentsMd = true;
+      console.log('  Keeping existing AGENTS.md (--keep)');
+    }
+    if (projectStatus.hasClaudeCommands) {
+      skipFiles.claudeCommands = true;
+      console.log('  Keeping existing .claude/commands/ (--keep)');
+    }
+    return skipFiles;
+  }
+
+  if (projectStatus.hasAgentsMd) {
+    const overwriteAgents = await askYesNo(question, 'Found existing AGENTS.md. Overwrite?', true);
+    skipFiles.agentsMd = !overwriteAgents;
+    console.log(overwriteAgents ? '  Will overwrite AGENTS.md' : '  Keeping existing AGENTS.md');
+  }
+
+  if (projectStatus.hasClaudeCommands) {
+    const overwriteCommands = await askYesNo(question, 'Found existing .claude/commands/. Overwrite?', true);
+    skipFiles.claudeCommands = !overwriteCommands;
+    console.log(overwriteCommands ? '  Will overwrite .claude/commands/' : '  Keeping existing .claude/commands/');
+  }
+
+  if (projectStatus.type !== 'fresh') {
+    console.log('');
+  }
+
+  return skipFiles;
+}
+
+// Helper: Load and setup canonical commands - extracted to reduce cognitive complexity
+
+
+// Helper: Load and setup canonical commands - extracted to reduce cognitive complexity
+async function loadAndSetupCanonicalCommands(selectedAgents, skipFiles) {
+  const claudeCommands = {};
+  const needsClaudeCommands = selectedAgents.includes('claude') ||
+    selectedAgents.some(a => AGENTS[a].needsConversion || AGENTS[a].copyCommands);
+
+  if (!needsClaudeCommands) {
+    return claudeCommands;
+  }
+
+  // First ensure Claude is set up
+  if (selectedAgents.includes('claude')) {
+    await setupAgent('claude', null, skipFiles);
+  }
+
+  // Then load the commands (from existing or newly created)
+  getWorkflowCommands().forEach(cmd => {
+    const cmdPath = path.join(projectRoot, `.claude/commands/${cmd}.md`);
+    const content = readFile(cmdPath);
+    if (content) {
+      claudeCommands[`${cmd}.md`] = content;
+    }
+  });
+
+  return claudeCommands;
+}
+
+// Helper: Setup all selected agents - extracted to reduce cognitive complexity
+
+
+// Helper: Setup all selected agents - extracted to reduce cognitive complexity
+async function setupSelectedAgents(selectedAgents, claudeCommands, skipFiles) {
+  const totalAgents = selectedAgents.length;
+  for (const [index, agentKey] of selectedAgents.entries()) {
+    const agent = AGENTS[agentKey];
+    console.log(`\n[${index + 1}/${totalAgents}] Setting up ${agent.name}...`);
+    if (agentKey !== 'claude') { // Claude already done above
+      await setupAgent(agentKey, claudeCommands, skipFiles);
+    }
+  }
+
+  console.log('');
+  console.log('Agent configuration complete!');
+  console.log('');
+  console.log('Installed for:');
+  selectedAgents.forEach(key => {
+    const agent = AGENTS[key];
+    console.log(`  * ${agent.name}`);
+  });
+}
+
+// Helper: Configure external services step - extracted to reduce cognitive complexity
+
+
+// Helper: Configure external services step - extracted to reduce cognitive complexity
+async function handleExternalServicesStep(flags, rl, question, selectedAgents, projectStatus) {
+  if (flags.skipExternal) {
+    console.log('');
+    console.log('Skipping external services configuration...');
+    return;
+  }
+
+  console.log('');
+  console.log('STEP 2: External Services (Optional)');
+  console.log('=====================================');
+  await configureExternalServices(rl, question, selectedAgents, projectStatus);
+}
+
+// Interactive setup with flag support
+
+
+// Interactive setup with flag support
+async function interactiveSetupWithFlags(flags) {
+  const rl = readline.createInterface({
+    input: process.stdin,
+    output: process.stdout
+  });
+
+  let setupCompleted = false;
+
+  // Handle Ctrl+C gracefully
+  rl.on('close', () => {
+    if (!setupCompleted) {
+      console.log('\n\nSetup cancelled.');
+      process.exit(0);
+    }
+  });
+
+  // Handle input errors
+  rl.on('error', (err) => {
+    console.error('Input error:', err.message);
+    process.exit(1);
+  });
+
+  const question = (prompt) => new Promise(resolve => rl.question(prompt, resolve));
+
+  showBanner('Agent Configuration');
+
+  // Show target directory
+  console.log(`  Target directory: ${process.cwd()}`);
+  console.log('  (Use --path <dir> to change target directory)');
+  console.log('');
+
+  // Check agent-independent prerequisites first
+  checkPrerequisites({
+    requireBeadsCli: true,
+    requireGithubCli: false,
+    requireJq: true,
+  });
+  console.log('');
+
+  // PROJECT DETECTION
+  const projectStatus = await detectProjectStatus();
+
+  // Handle user-provided flags to override auto-detection
+  handleFlagsOverride(flags, projectStatus);
+
+  // Display existing installation status
+  displayExistingInstallation(projectStatus);
+
+  // Prompt for overwrite decisions
+  const skipFiles = await promptForOverwriteDecisions(question, projectStatus, flags);
+
+  // Agent auto-detection (suggests but does not force)
+  const envDetection = detectEnvironment(projectRoot);
+  if (envDetection.activeAgent && envDetection.confidence === 'high') {
+    console.log(`  Detected: ${envDetection.activeAgent} (${envDetection.activeAgentSource})`);
+  }
+  if (envDetection.configuredAgents.length > 0) {
+    console.log(`  Previously configured: ${envDetection.configuredAgents.join(', ')}`);
+  }
+
+  // STEP 1: Agent Selection (delegated to helper)
+  const agentKeys = Object.keys(AGENTS);
+  const selectedAgents = await promptForAgentSelection(question, agentKeys);
+
+  // Check GitHub CLI prerequisite now that selectedAgents is known
+  if (requiresGithubCliForSetup(selectedAgents, { syncEnabled: SYNC_ENABLED })) {
+    checkPrerequisites({ requireGithubCli: true });
+  }
+
+  console.log('');
+  console.log('Installing Forge workflow...');
+
+  // Setup AGENTS.md (delegated to helper)
+  setupAgentsMdFile(flags, skipFiles);
+  console.log('');
+
+  // Setup core documentation
+  setupCoreDocs();
+  console.log('');
+
+  // Load Claude commands if needed (delegated to helper)
+  const claudeCommands = await loadAndSetupCanonicalCommands(selectedAgents, skipFiles);
+
+  // Setup each selected agent with progress indication (delegated to helper)
+  await setupSelectedAgents(selectedAgents, claudeCommands, skipFiles);
+  ensureWorkflowRuntimeAssets(selectedAgents);
+
+  // Handle external services step (delegated to helper)
+  await handleExternalServicesStep(flags, rl, question, selectedAgents, projectStatus);
+
+  setupCompleted = true;
+  rl.close();
+
+  // Display final summary (delegated to helper)
+  displaySetupSummary(selectedAgents);
+}
+
+// Main
+// Helper: Handle --path setup
+
+
+// Main
+// Helper: Handle --path setup
+function handlePathSetup(targetPath) {
+  const resolvedPath = path.resolve(targetPath);
+
+  // Create directory if it doesn't exist
+  if (!fs.existsSync(resolvedPath)) {
+    try {
+      fs.mkdirSync(resolvedPath, { recursive: true });
+      console.log(`Created directory: ${resolvedPath}`);
+    } catch (err) {
+      console.error(`Error creating directory: ${err.message}`);
+      process.exit(1);
+    }
+  }
+
+  // Verify it's a directory
+  if (!fs.statSync(resolvedPath).isDirectory()) {
+    console.error(`Error: ${resolvedPath} is not a directory`);
+    process.exit(1);
+  }
+
+  // Change to target directory
+  try {
+    process.chdir(resolvedPath);
+    console.log(`Working directory: ${resolvedPath}`);
+    console.log('');
+  } catch (err) {
+    console.error(`Error changing to directory: ${err.message}`);
+    process.exit(1);
+  }
+
+  // Return the resolved path so caller can update projectRoot
+  return resolvedPath;
+}
+
+// Helper: Determine selected agents from flags
+
+
+// Helper: Determine selected agents from flags
+function determineSelectedAgents(flags) {
+  if (flags.all) {
+    return Object.keys(AGENTS);
+  }
+
+  if (flags.agents) {
+    const selectedAgents = validateAgents(flags.agents);
+    if (selectedAgents.length === 0) {
+      console.log('No valid agents specified.');
+      console.log('Available agents:', Object.keys(AGENTS).join(', '));
+      process.exit(1);
+    }
+    return selectedAgents;
+  }
+
+  return [];
+}
+
+// Shared setup executor — used by handleSetupCommand
+
+// Dry-run setup — enumerate planned actions without writing files
+
+
+// Shared setup executor — used by handleSetupCommand
+
+// Dry-run setup — enumerate planned actions without writing files
+function dryRunSetup(agents) { // NOSONAR — Extracted as-is from bin/forge.js; complexity reduction deferred
+  const collector = new ActionCollector();
+
+  // Helper: add create or skip based on whether file exists
+  function addFileAction(relPath, description) {
+    const absPath = path.join(projectRoot, relPath);
+    if (fs.existsSync(absPath)) {
+      collector.add('skip', relPath, 'Already exists');
+    } else {
+      collector.add('create', relPath, description);
+    }
+  }
+
+  // AGENTS.md
+  addFileAction('AGENTS.md', 'Copy workflow documentation');
+
+  // Per-agent planned actions
+  for (const agentKey of agents) {
+    const agent = AGENTS[agentKey];
+    if (!agent) continue;
+
+    // Agent directories
+    for (const dir of agent.dirs) {
+      addFileAction(dir + '/', 'Create agent directory');
+    }
+
+    // Claude-specific files
+    if (agentKey === 'claude') {
+      const cmds = getWorkflowCommands();
+      for (const cmd of cmds) {
+        addFileAction(`.claude/commands/${cmd}.md`, 'Workflow command');
+      }
+      addFileAction('.claude/rules/workflow.md', 'Workflow rules');
+      addFileAction('.claude/scripts/load-env.sh', 'Environment loader script');
+      addFileAction('.claude/skills/forge-workflow/SKILL.md', 'Forge workflow skill');
+      addFileAction('.mcp.json', 'MCP server configuration');
+      addFileAction('CLAUDE.md', 'Claude root config (links to AGENTS.md)');
+    }
+
+    if (needsWorkflowRuntimeAssets([agentKey])) {
+      for (const assetPath of getWorkflowRuntimeAssets()) {
+        addFileAction(assetPath, 'Workflow runtime asset');
+      }
+    }
+
+    // Cursor-specific files
+    if (agent.customSetup === 'cursor') {
+      addFileAction('.cursor/rules/forge-workflow.mdc', 'Cursor workflow rule');
+      addFileAction('.cursor/rules/tdd-enforcement.mdc', 'Cursor TDD rule');
+      addFileAction('.cursor/rules/security-scanning.mdc', 'Cursor security rule');
+      addFileAction('.cursor/rules/documentation.mdc', 'Cursor documentation rule');
+    }
+
+    if (agentKey === 'kilocode') {
+      addFileAction('.kilocode/workflows/forge-workflow.md', 'Kilo native workflow');
+      addFileAction('.kilocode/rules/workflow.md', 'Kilo native rules');
+      addFileAction('.kilocode/skills/forge-workflow/SKILL.md', 'Kilo native skill');
+    }
+
+    if (agent.customSetup === 'copilot') {
+      addFileAction('.github/copilot-instructions.md', 'Copilot root instructions');
+      addFileAction('.github/instructions/typescript.instructions.md', 'Copilot TypeScript instructions');
+      addFileAction('.github/instructions/testing.instructions.md', 'Copilot testing instructions');
+      addFileAction('.github/prompts/red.prompt.md', 'Copilot RED prompt');
+      addFileAction('.github/prompts/green.prompt.md', 'Copilot GREEN prompt');
+    }
+
+    if (agent.customSetup === 'opencode') {
+      addFileAction('opencode.json', 'OpenCode root config');
+      addFileAction('.opencode/agents/plan-review.md', 'OpenCode plan-review agent');
+      addFileAction('.opencode/agents/tdd-build.md', 'OpenCode tdd-build agent');
+    }
+
+    // Agent commands (converted from Claude format)
+    if (agent.needsConversion || agent.copyCommands || agent.promptFormat) {
+      const cmds = getWorkflowCommands();
+      const targetDir = agent.dirs[0];
+      for (const cmd of cmds) {
+        const ext = agent.promptFormat ? '.prompt.md' : '.md';
+        addFileAction(`${targetDir}/${cmd}${ext}`, 'Converted workflow command');
+      }
+    }
+
+    // Agent rules (copied from Claude)
+    if (agent.needsConversion) {
+      const rulesDir = agent.dirs.find(d => d.includes('/rules'));
+      if (rulesDir) {
+        addFileAction(`${rulesDir}/workflow.md`, 'Workflow rules');
+      }
+    }
+
+    // Agent skill
+    if (agentKey === 'codex') {
+      const skillEntries = listCodexSkillEntries(packageDir);
+      for (const entry of skillEntries) {
+        addFileAction(path.join(entry.dir, entry.filename), 'Codex stage skill');
+      }
+    } else if (agent.hasSkill) {
+      const skillDir = agent.dirs.find(d => d.includes('/skills/'));
+      if (skillDir) {
+        addFileAction(`${skillDir}/SKILL.md`, 'Forge workflow skill');
+      }
+    }
+
+    // Agent link file (symlink or copy of AGENTS.md)
+    if (shouldLinkAgentsMd(agent)) {
+      addFileAction(agent.linkFile, 'Link to AGENTS.md');
+    }
+  }
+
+  // Git hooks
+  addFileAction('lefthook.yml', 'Git hook configuration');
+  addFileAction('.forge/hooks/check-tdd.js', 'TDD enforcement hook');
+
+  // Print dry-run summary
+  console.log('');
+  console.log('Dry-run: the following actions would be performed:');
+  console.log('');
+  collector.print();
+  console.log('');
+  console.log(`Total: ${collector.list().length} planned actions`);
+  console.log('No files were modified.');
+}
+
+
+
+async function executeSetup(config) {
+  const { agents, skipExternal, keepExisting = false, commandRunner } = config;
+
+  showBanner('Installing for specified agents...');
+  console.log('');
+
+  // Check prerequisites
+  checkPrerequisites({
+    requireBeadsCli: true,
+    requireGithubCli: requiresGithubCliForSetup(agents, { syncEnabled: SYNC_ENABLED }),
+    requireJq: true,
+    commandRunner,
+  });
+  console.log('');
+
+  // Copy AGENTS.md (only if not exists — preserve user customizations; actionLog tracks it)
+  const agentsDest = path.join(projectRoot, 'AGENTS.md');
+  if (fs.existsSync(agentsDest)) {
+    actionLog.add('AGENTS.md', 'skipped', 'already exists');
+  } else {
+    const agentsSrc = path.join(packageDir, 'AGENTS.md');
+    copyFile(agentsSrc, 'AGENTS.md');
+  }
+  console.log('');
+
+  // Setup core documentation
+  setupCoreDocs();
+  console.log('');
+
+  const skipFiles = {
+    agentsMd: keepExisting && fs.existsSync(path.join(projectRoot, 'AGENTS.md')),
+    claudeCommands: keepExisting && fs.existsSync(path.join(projectRoot, '.claude', 'commands'))
+  };
+
+  if (skipFiles.claudeCommands) {
+    console.log('  Keeping existing .claude/commands/ (--keep)');
+  }
+
+  // Load canonical commands — use loadAndSetupCanonicalCommands when claude is selected
+  // so that .claude/commands/ are seeded before reading them
+  const claudeCommands = agents.includes('claude')
+    ? await loadAndSetupCanonicalCommands(agents, skipFiles)
+    : loadClaudeCommands(agents);
+
+  // Setup agents with progress output (setupSelectedAgents skips claude internally
+  // since loadAndSetupCanonicalCommands already handled it above)
+  await setupSelectedAgents(agents, claudeCommands, skipFiles);
+  ensureWorkflowRuntimeAssets(agents);
+  ensureWorkflowShellPolicy(agents);
+  repairDeclaredLefthookDependency(agents);
+
+  // Detect Husky and migrate before installing Lefthook hooks
+  await handleHuskyMigration();
+
+  // Install git hooks for TDD enforcement
+  console.log('');
+  installGitHooks();
+
+  // External services (unless skipped)
+  await handleExternalServices(skipExternal, agents);
+
+  // --sync flag: scaffold Beads GitHub sync workflows without prompting
+  if (SYNC_ENABLED) {
+    await handleSyncScaffold();
+  }
+
+  // Progressive setup summary
+  console.log('');
+  console.log(renderSetupSummary(actionLog, agents, VERBOSE_MODE));
+  console.log('');
+}
+
+// Helper: Scaffold Beads GitHub sync when --sync flag is provided
+
+
+// Helper: Scaffold Beads GitHub sync when --sync flag is provided
+async function handleSyncScaffold() {
+  console.log('');
+  console.log('Scaffolding Beads GitHub sync workflows (--sync)...');
+  try {
+    // Scaffold sync files using the new lib module
+    const result = scaffoldBeadsSync(projectRoot, packageDir);
+    for (const f of (result.filesCreated || [])) {
+      console.log(`  Created: ${f}`);
+    }
+    for (const f of (result.filesSkipped || [])) {
+      console.log(`  Skipped: ${f} (already exists)`);
+    }
+
+    // Detect default branch and Beads version, then template workflows
+    const branch = detectDefaultBranch(projectRoot);
+    const beadsVersion = detectBeadsVersion();
+    const workflowDir = path.join(projectRoot, '.github', 'workflows');
+    templateWorkflows(workflowDir, branch, beadsVersion, result.filesCreated || []);
+    console.log(`  Branch: ${branch}, Beads version: ${beadsVersion}`);
+
+    // PAT setup: interactive when possible, reminder otherwise
+    try {
+      const patResult = setupPAT(projectRoot, { interactive: !NON_INTERACTIVE });
+      if (patResult.success) {
+        console.log('  PAT configured for Beads sync');
+      } else if (patResult.reminder) {
+        console.log(`  ${patResult.reminder}`);
+      } else if (patResult.instructions) {
+        console.log(`  ${patResult.instructions.split('\n')[0]}`);
+      }
+    } catch (_patErr) { // NOSONAR — best-effort PAT setup, non-fatal
+      // PAT setup is best-effort — don't block sync scaffold
+    }
+  } catch (err) {
+    console.error(`  Error scaffolding GitHub-Beads sync: ${err.message}`);
+  }
+}
+
+// Helper: Handle setup command in non-quick mode
+
+
+// Helper: Handle setup command in non-quick mode
+async function handleSetupCommand(selectedAgents, flags) {
+  if (!Array.isArray(selectedAgents) || selectedAgents.length === 0) {
+    return interactiveSetupWithFlags(flags);
+  }
+
+  // Allow callers (e.g. reinstall) to override projectRoot without process.chdir()
+  const savedRoot = projectRoot;
+  if (flags.projectRoot) {
+    projectRoot = flags.projectRoot;
+  }
+  try {
+    await executeSetup({
+      agents: selectedAgents,
+      skipExternal: flags.skipExternal,
+      keepExisting: flags.keep,
+      commandRunner: flags.commandRunner,
+    });
+  } finally {
+    projectRoot = savedRoot;
+  }
+}
+
+// Helper: Handle external services configuration
+
+
+// Helper: Handle external services configuration
+async function handleExternalServices(skipExternal, selectedAgents) {
+  if (skipExternal) {
+    console.log('');
+    console.log('Skipping external services configuration...');
+    return;
+  }
+
+  const rl = readline.createInterface({
+    input: process.stdin,
+    output: process.stdout
+  });
+
+  let setupCompleted = false;
+  rl.on('close', () => {
+    if (!setupCompleted) {
+      console.log('\n\nSetup cancelled.');
+      process.exit(0);
+    }
+  });
+
+  const question = (prompt) => new Promise(resolve => rl.question(prompt, resolve));
+  await configureExternalServices(rl, question, selectedAgents);
+  setupCompleted = true;
+  rl.close();
+}
+
+
+/**
+ * Detect which agents are already configured in a project directory.
+ * Checks for the presence of each agent's configured directories/files.
+ * Returns the external-facing setup IDs used by the setup UX, including
+ * legacy aliases such as `claude-code`, `github-copilot`, and `roo-code`.
+ * Callers that need raw plugin IDs for internal lookup must normalize first.
+ *
+ * @param {string} dir - Project directory to scan
+ * @returns {string[]} External-facing setup agent IDs with configuration present
+ */
+function detectConfiguredAgents(dir) {
+  const pluginManager = new PluginManager();
+  const detected = [];
+  const legacyAgentIds = {
+    claude: 'claude-code',
+    copilot: 'github-copilot',
+    roo: 'roo-code',
+  };
+
+  pluginManager.getAllPlugins().forEach((plugin, id) => {
+    const dirs = Object.values(plugin.directories || {});
+    const files = Object.values(plugin.files || {});
+    const markers = [...dirs, ...files].filter(Boolean);
+    const isConfigured = markers.some((marker) => fs.existsSync(path.join(dir, marker)));
+
+    if (isConfigured) {
+      detected.push(legacyAgentIds[id] || id);
+    }
+  });
+
+  return detected;
+}
+
+/**
+ * Remove agent-specific files from a project directory.
+ * Used during setup --clean or reset flows.
+ *
+ * @param {string} dir - Project directory
+ * @param {string} agentName - Agent slug (e.g. 'cursor', 'cline')
+ * @param {object} [manifest] - Optional sync manifest with file paths to remove
+ * @returns {{ removed: string[], errors: string[] }}
+ */
+function removeAgentFiles(dir, agentName, manifest) {
+  const removed = [];
+  const errors = [];
+
+  // Validate agent name (OWASP A03 — path traversal prevention)
+  if (!/^[a-z0-9-]+$/.test(agentName)) {
+    errors.push(`Invalid agent name: "${agentName}"`);
+    return { removed, errors };
+  }
+
+  const agent = AGENTS[agentName];
+  if (!agent) {
+    errors.push(`Unknown agent: "${agentName}"`);
+    return { removed, errors };
+  }
+
+  // Remove command files from manifest if provided
+  if (manifest && Array.isArray(manifest.files)) {
+    for (const relPath of manifest.files) {
+      // Only remove files belonging to this agent
+      const agentDirs = agent.dirs || [];
+      const belongsToAgent = agentDirs.some(d => relPath.startsWith(d));
+      if (!belongsToAgent) continue;
+
+      const absPath = path.join(dir, relPath);
+      try {
+        if (fs.existsSync(absPath)) {
+          fs.unlinkSync(absPath);
+          removed.push(relPath);
+        }
+      } catch (err) {
+        errors.push(`Failed to remove ${relPath}: ${err.message}`);
+      }
+    }
+  }
+
+  return { removed, errors };
+}
+
+/**
+ * Parse setup-related CLI flags from argv.
+ * Extracts --agents, --all, --detect, --keep, --yes, etc.
+ *
+ * @param {string[]} argv - Process argv (typically process.argv.slice(2))
+ * @returns {object} Parsed flags object
+ */
+const SETUP_FLAG_DEFAULTS = Object.freeze({
+  agents: null,
+  all: false,
+  detect: false,
+  keep: false,
+  yes: false,
+  force: false,
+  verbose: false,
+  dryRun: false,
+  quick: false,
+  skipExternal: false,
+  sync: false,
+  symlink: false,
+  nonInteractive: false,
+});
+
+const SIMPLE_SETUP_FLAG_UPDATES = Object.freeze({
+  '--all': { all: true },
+  '--detect': { detect: true },
+  '--keep': { keep: true },
+  '--force': { force: true },
+  '--verbose': { verbose: true },
+  '--dry-run': { dryRun: true },
+  '--quick': { quick: true },
+  '--skip-external': { skipExternal: true },
+  '--sync': { sync: true },
+  '--symlink': { symlink: true },
+  '--yes': { yes: true, nonInteractive: true },
+  '-y': { yes: true, nonInteractive: true },
+});
+
+function parseAgentFlag(argv, currentIndex, isFlagToken) {
+  const arg = argv[currentIndex];
+  if (arg === '--agents' && currentIndex + 1 < argv.length && !isFlagToken(argv[currentIndex + 1])) {
+    const agentTokens = [];
+    let nextIndex = currentIndex;
+    while (nextIndex + 1 < argv.length && !isFlagToken(argv[nextIndex + 1])) {
+      agentTokens.push(argv[++nextIndex]);
+    }
+    return { handled: true, nextIndex, agents: agentTokens.join(',') };
+  }
+
+  if (arg.startsWith('--agents=')) {
+    return { handled: true, nextIndex: currentIndex, agents: arg.split('=')[1] };
+  }
+
+  return { handled: false, nextIndex: currentIndex, agents: null };
+}
+
+function applySimpleSetupFlag(flags, arg) {
+  const updates = SIMPLE_SETUP_FLAG_UPDATES[arg];
+  if (!updates) {
+    return false;
+  }
+
+  Object.assign(flags, updates);
+  return true;
+}
+
+function parseSetupFlags(argv) {
+  const flags = { ...SETUP_FLAG_DEFAULTS };
+
+  const isFlagToken = (token) => typeof token === 'string' && token.startsWith('-');
+
+  for (let i = 0; i < argv.length; i++) {
+    const arg = argv[i];
+    const agentResult = parseAgentFlag(argv, i, isFlagToken);
+    if (agentResult.handled) {
+      flags.agents = agentResult.agents;
+      i = agentResult.nextIndex;
+      continue;
+    }
+
+    applySimpleSetupFlag(flags, arg);
+  }
+
+  return flags;
+}
+
+/**
+ * Merge setup-specific runtime flags from raw argv into the global CLI flags.
+ * This lets the extracted setup command own setup-only flags without relying
+ * on bin/forge.js to keep a duplicate parser in sync.
+ *
+ * @param {Record<string, unknown>} flags
+ * @param {string[]} argv
+ * @returns {Record<string, unknown>}
+ */
+function mergeSetupFlags(flags, argv) {
+  const setupFlags = parseSetupFlags(argv);
+  return {
+    ...flags,
+    agents: flags.agents ?? setupFlags.agents,
+    all: Boolean(flags.all || setupFlags.all),
+    detect: Boolean(flags.detect || setupFlags.detect),
+    keep: Boolean(flags.keep || setupFlags.keep),
+    yes: Boolean(flags.yes || setupFlags.yes),
+    force: Boolean(flags.force || setupFlags.force),
+    verbose: Boolean(flags.verbose || setupFlags.verbose),
+    dryRun: Boolean(flags.dryRun || setupFlags.dryRun),
+    quick: Boolean(flags.quick || setupFlags.quick),
+    skipExternal: Boolean(flags.skipExternal || setupFlags.skipExternal),
+    sync: Boolean(flags.sync || setupFlags.sync),
+    symlink: Boolean(flags.symlink || setupFlags.symlink),
+    nonInteractive: Boolean(flags.nonInteractive || setupFlags.nonInteractive),
+  };
+}
+
+function normalizeDetectedAgent(agentName) {
+  const aliases = {
+    'claude-code': 'claude',
+    'github-copilot': 'copilot',
+    'kilo-code': 'kilocode',
+    'roo-code': 'roo',
+  };
+  return aliases[agentName] || agentName;
+}
+
+function detectAgentsFromRuntime() {
+  const envDetection = detectEnvironment(projectRoot);
+  const detected = new Set();
+
+  for (const agentName of envDetection.configuredAgents || []) {
+    const normalized = normalizeDetectedAgent(agentName);
+    if (AGENTS[normalized]) {
+      detected.add(normalized);
+    }
+  }
+
+  if (detected.size === 0 && envDetection.activeAgent) {
+    const normalized = normalizeDetectedAgent(envDetection.activeAgent);
+    if (AGENTS[normalized]) {
+      detected.add(normalized);
+    }
+  }
+
+  return [...detected];
+}
+
+// --- Registry-compliant exports ---
+module.exports = {
+  name: 'setup',
+  description: 'Initialize forge in a project',
+  handler: async (args, flags, root) => { // NOSONAR — Extracted as-is from bin/forge.js; complexity reduction deferred
+    flags = mergeSetupFlags(flags, args);
+
+    // Sync module state from caller
+    if (root) projectRoot = root;
+    if (flags.force) FORCE_MODE = true;
+    if (flags.verbose) VERBOSE_MODE = true;
+    if (flags.nonInteractive || flags.yes) NON_INTERACTIVE = true;
+    if (flags.symlink) SYMLINK_ONLY = true;
+    if (flags.sync) SYNC_ENABLED = true;
+    actionLog = new SetupActionLog();
+    PKG_MANAGER = detectPackageManager();
+
+    // Determine agents to install
+    let selectedAgents = determineSelectedAgents(flags);
+
+    if (flags.detect && selectedAgents.length === 0) {
+      selectedAgents = detectAgentsFromRuntime();
+      if (selectedAgents.length > 0) {
+        console.log(`Auto-detected agents (--detect): ${selectedAgents.join(', ')}`);
+      } else {
+        console.log('No agents detected via --detect; falling back to interactive selection.');
+      }
+    }
+
+    if (flags.yes && selectedAgents.length === 0) {
+      selectedAgents = ['claude'];
+    }
+    if (flags.yes) {
+      flags.skipExternal = true;
+    }
+
+    if (flags.dryRun) {
+      if (selectedAgents.length === 0) selectedAgents = ['claude'];
+      dryRunSetup(selectedAgents);
+      return { success: true };
+    }
+
+    if (flags.quick) {
+      flags.skipExternal = true;
+      if (selectedAgents.length === 0 || (flags.yes && !flags.agents)) {
+        selectedAgents = Object.keys(AGENTS);
+      }
+      await quickSetup(selectedAgents, flags.skipExternal);
+      return { success: true };
+    }
+
+    if (selectedAgents.length > 0) {
+      await handleSetupCommand(selectedAgents, flags);
+      return { success: true };
+    }
+
+    await interactiveSetupWithFlags(flags);
+    return { success: true };
+  },
+
+  // Expose internals for testing and cross-command use
+  checkPrerequisites,
+  setupCoreDocs,
+  displaySetupSummary,
+  setupAgent,
+  quickSetup,
+  interactiveSetupWithFlags,
+  dryRunSetup,
+  handleSetupCommand,
+  executeSetup,
+  handleExternalServices,
+  _interactiveSetup,
+  configureExternalServices,
+  configureDefaultExternalServices,
+  installBeadsWithMethod,
+  installSkillsWithMethod,
+  installViaBunx,
+  autoInstallLefthook,
+  autoSetupToolsInQuickMode,
+  setupClaudeMcpConfig,
+  displayMcpStatus,
+  displayEnvTokenResults,
+  minimalInstall,
+  determineSelectedAgents,
+  handlePathSetup,
+  loadAndSetupCanonicalCommands,
+  detectConfiguredAgents,
+  removeAgentFiles,
+  parseSetupFlags,
+  mergeSetupFlags,
+  getWorkflowCommands,
+  getWorkflowRuntimeAssets,
+  findMissingWorkflowRuntimeAssets,
+  ensureWorkflowShellPolicy,
+  repairWorkflowRuntimeAssets,
+  repairRuntimeReadiness,
+  _showBanner: showBanner,
+
+  // State accessors for testing
+  _getState: () => ({ projectRoot, FORCE_MODE, VERBOSE_MODE, NON_INTERACTIVE, SYMLINK_ONLY, SYNC_ENABLED, PKG_MANAGER }),
+  _setState: (state) => {
+    if (state.projectRoot !== undefined) projectRoot = state.projectRoot;
+    if (state.FORCE_MODE !== undefined) FORCE_MODE = state.FORCE_MODE;
+    if (state.VERBOSE_MODE !== undefined) VERBOSE_MODE = state.VERBOSE_MODE;
+    if (state.NON_INTERACTIVE !== undefined) NON_INTERACTIVE = state.NON_INTERACTIVE;
+    if (state.SYMLINK_ONLY !== undefined) SYMLINK_ONLY = state.SYMLINK_ONLY;
+    if (state.SYNC_ENABLED !== undefined) SYNC_ENABLED = state.SYNC_ENABLED;
+    if (state.PKG_MANAGER !== undefined) PKG_MANAGER = state.PKG_MANAGER;
+  },
+};