nexus-agents 2.55.0 → 2.56.0

package/dist/chunk-KGMC6F5D.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/setup-command.ts","../src/cli/setup-types.ts","../src/cli/setup-environment.ts","../src/cli/setup-mcp.ts","../src/cli/setup-rules.ts","../src/cli/setup-formatting.ts","../src/cli/setup-opencode.ts","../src/cli/setup-gemini.ts","../src/cli/setup-codex.ts","../src/cli/setup-wizard.ts","../src/cli/setup-permissions.ts","../src/cli/verify-command.ts"],"sourcesContent":["/* eslint-disable max-lines -- Cohesive setup command module (governance: 400-600 OK if cohesive) */\n/**\n * nexus-agents setup command\n *\n * Configures Claude CLI integration with nexus-agents MCP server.\n * Generates MCP configuration snippet and .rules/nexus-agents.md.\n *\n * @module cli/setup-command\n * (Source: Issue #363 - Auto-configure Claude CLI integration)\n * (Source: Issue #425 - Interactive setup wizard)\n */\n\nimport { existsSync } from 'node:fs';\nimport type { SetupOptions, SetupResult, SetupStep, EnvironmentInfo } from './setup-types.js';\nimport { SetupOptionsSchema } from './setup-types.js';\nimport { getTimeProvider, getErrorMessage } from '../core/index.js';\nimport {\n  detectEnvironment,\n  generateMcpSnippet,\n  generateRulesContent,\n  createRulesFile,\n  getRulesFilePath,\n  formatStatus,\n  formatHeader,\n  formatCodeBlock,\n  isInteractive,\n  configureMcpServer,\n  // Hook configuration (Issue #416)\n  configureHooks,\n  generateHookSnippet,\n} from './setup-helpers.js';\nimport type { McpConfigResult, HookConfigResult } from './setup-helpers.js';\nimport { initDataDirectories } from './setup-data-dir.js';\nimport type { DataDirInitResult } from './setup-data-dir.js';\nimport { runConfigInitSync } from './setup-config.js';\nimport { detectOpenCodeCli, configureOpenCode } from './setup-opencode.js';\nimport { detectGeminiCli, configureGemini } from './setup-gemini.js';\nimport { detectCodexCli, configureCodex } from './setup-codex.js';\nimport { VERSION } from '../version.js';\nimport { runWizard } from './setup-wizard.js';\nimport { generatePermissionsSnippet, buildPermissionsBanner } from './setup-permissions.js';\n// #2137: post-setup health gate. Surfaces install-time issues that are easy\n// to miss (better-sqlite3 native build, missing API keys, unwritable data\n// dirs) inline at the end of setup, with copy-pasteable remediation.\nimport { runVerify } from './verify-command.js';\nimport { colors, symbols } from './ansi-output.js';\n\n// ============================================================================\n// Output Helpers\n// ============================================================================\n\n/**\n * Writes a line to stdout.\n */\nfunction writeLine(text: string): void {\n  process.stdout.write(text + '\\n');\n}\n\n/**\n * Writes an empty line.\n */\nfunction writeEmptyLine(): void {\n  process.stdout.write('\\n');\n}\n\n/**\n * Prints MCP configuration result section.\n */\nfunction printMcpResult(mcpResult: McpConfigResult, snippet: string | undefined): void {\n  writeLine(formatHeader('MCP Configuration'));\n  writeLine('─'.repeat(40));\n  if (mcpResult.success) {\n    writeLine(mcpResult.message);\n    writeLine('Run `/mcp` in Claude Code to verify.');\n  } else {\n    writeLine(`Failed: ${mcpResult.message}`);\n    if (snippet !== undefined) {\n      writeEmptyLine();\n      writeLine('Manual fallback - run:');\n      writeEmptyLine();\n      writeLine(formatCodeBlock(`claude mcp add-json nexus-agents '${snippet}'`));\n    }\n  }\n  writeEmptyLine();\n}\n\n/**\n * Prints rules file section.\n */\nfunction printRulesFile(rulesPath: string): void {\n  writeLine(formatHeader('Rules File'));\n  writeLine('─'.repeat(40));\n  writeLine(`Created: ${rulesPath}`);\n  writeLine('Claude will now have context about nexus-agents tools.');\n  writeEmptyLine();\n}\n\n/**\n * Prints hooks configuration result section.\n * (Source: Issue #416)\n */\nfunction printHooksResult(hookResult: HookConfigResult, snippet: string | undefined): void {\n  writeLine(formatHeader('Hooks Configuration'));\n  writeLine('─'.repeat(40));\n  if (hookResult.success) {\n    writeLine(hookResult.message);\n    writeLine('Hooks will track sessions, metrics, and validate tool use.');\n  } else {\n    writeLine(`Note: ${hookResult.message}`);\n    if (snippet !== undefined) {\n      writeEmptyLine();\n      writeLine('Manual fallback - add to ~/.claude/settings.json:');\n      writeEmptyLine();\n      writeLine(formatCodeBlock(snippet));\n    }\n  }\n  writeEmptyLine();\n}\n\n/**\n * Prints warnings section.\n */\nfunction printWarnings(warnings: readonly string[]): void {\n  writeLine(formatHeader('Warnings'));\n  writeLine('─'.repeat(40));\n  for (const warning of warnings) {\n    writeLine(`⚠ ${warning}`);\n  }\n  writeEmptyLine();\n}\n\n/**\n * Prints errors section.\n */\nfunction printErrors(errors: readonly string[]): void {\n  writeLine(formatHeader('Errors'));\n  writeLine('─'.repeat(40));\n  for (const error of errors) {\n    writeLine(`✗ ${error}`);\n  }\n  writeEmptyLine();\n}\n\n/**\n * Prints next steps section.\n */\nfunction printNextSteps(mcpConfigured: boolean, hasMcpSnippet: boolean): void {\n  writeLine(formatHeader('Next Steps'));\n  writeLine('─'.repeat(40));\n  if (hasMcpSnippet && !mcpConfigured) {\n    writeLine('1. Configure MCP manually (see above)');\n    writeLine('2. Restart Claude Code');\n  }\n  writeLine('3. Run: nexus-agents doctor');\n  writeLine('4. Try: nexus-agents orchestrate \"Hello World\"');\n  writeEmptyLine();\n}\n\n/**\n * Prints steps with status indicators.\n */\nfunction printSteps(steps: readonly SetupStep[], verbose: boolean): void {\n  for (const step of steps) {\n    const status = formatStatus(step.status);\n    const duration = step.durationMs !== undefined ? ` (${String(step.durationMs)}ms)` : '';\n    writeLine(`${status} ${step.name}${verbose ? duration : ''}`);\n    if (step.message !== undefined && (verbose || step.status === 'failed')) {\n      writeLine(`  ${step.message}`);\n    }\n  }\n  writeEmptyLine();\n}\n\n/**\n * Prints result summary line.\n */\nfunction printSummary(success: boolean): void {\n  const summary = success ? '✓ Setup completed successfully!' : '✗ Setup completed with errors';\n  writeLine(success ? `\\x1b[32m${summary}\\x1b[0m` : `\\x1b[31m${summary}\\x1b[0m`);\n  writeEmptyLine();\n}\n\n// ============================================================================\n// Setup Steps\n// ============================================================================\n\n/**\n * Runs the environment detection step.\n */\nfunction runDetectionStep(projectRoot: string): { env: EnvironmentInfo; step: SetupStep } {\n  const time = getTimeProvider();\n  const startTime = time.now();\n  const env = detectEnvironment(projectRoot);\n\n  return {\n    env,\n    step: {\n      name: 'Environment Detection',\n      status: 'success',\n      message: `Platform: ${env.platform}, Claude CLI: ${env.claudeCli.installed ? (env.claudeCli.version ?? 'installed') : 'not found'}`,\n      durationMs: time.now() - startTime,\n    },\n  };\n}\n\n/** Minimum Node.js major version required. */\nconst REQUIRED_NODE_MAJOR = 22;\n\n/**\n * Runs the prerequisite validation step.\n * Checks Node.js version and warns about missing package managers.\n */\nfunction runPrerequisiteStep(): { step: SetupStep; warnings: readonly string[] } {\n  const time = getTimeProvider();\n  const startTime = time.now();\n  const warnings: string[] = [];\n\n  const version = process.version;\n  const major = Number(version.slice(1).split('.')[0]);\n  const nodeOk = major >= REQUIRED_NODE_MAJOR;\n\n  if (!nodeOk) {\n    warnings.push(\n      `Node.js ${version} detected — v${String(REQUIRED_NODE_MAJOR)}.x+ required. Some features may not work.`\n    );\n  }\n\n  const status = nodeOk ? 'success' : 'warning';\n  const message = nodeOk\n    ? `Node.js ${version} (meets v${String(REQUIRED_NODE_MAJOR)}.x requirement)`\n    : `Node.js ${version} — v${String(REQUIRED_NODE_MAJOR)}.x+ required`;\n\n  return {\n    step: {\n      name: 'Prerequisite Check',\n      status,\n      message,\n      durationMs: time.now() - startTime,\n    },\n    warnings,\n  };\n}\n\n/** MCP step result type. */\ntype McpStepResult = {\n  step: SetupStep;\n  snippet: string | undefined;\n  mcpResult: McpConfigResult | undefined;\n};\n\n/** Creates an MCP step result. */\nfunction makeMcpResult(\n  status: SetupStep['status'],\n  message: string,\n  startTime: number,\n  snippet?: string,\n  mcpResult?: McpConfigResult\n): McpStepResult {\n  return {\n    step: {\n      name: 'MCP Configuration',\n      status,\n      message,\n      durationMs: getTimeProvider().now() - startTime,\n    },\n    snippet,\n    mcpResult,\n  };\n}\n\n/**\n * Runs the MCP configuration step.\n */\nfunction runMcpConfigStep(env: EnvironmentInfo, options: SetupOptions): McpStepResult {\n  const startTime = getTimeProvider().now();\n\n  if (options.skipMcp) {\n    return makeMcpResult('skipped', 'Skipped (--skip-mcp)', startTime);\n  }\n\n  const useNpx = !env.claudeCli.installed;\n  const snippet = generateMcpSnippet(useNpx);\n\n  if (!env.claudeCli.installed) {\n    const mcpResult: McpConfigResult = {\n      success: false,\n      alreadyConfigured: false,\n      message: 'Claude CLI not installed',\n    };\n    return makeMcpResult(\n      'warning',\n      'Claude CLI not found - manual configuration required',\n      startTime,\n      snippet,\n      mcpResult\n    );\n  }\n\n  const mcpResult = configureMcpServer(useNpx, options.force, options.scope);\n  const status = mcpResult.success\n    ? mcpResult.alreadyConfigured\n      ? 'skipped'\n      : 'success'\n    : 'failed';\n  return makeMcpResult(\n    status,\n    mcpResult.message,\n    startTime,\n    mcpResult.success ? undefined : snippet,\n    mcpResult\n  );\n}\n\n/** Creates a rules step result. */\nfunction makeRulesResult(\n  status: SetupStep['status'],\n  message: string,\n  startTime: number,\n  rulesPath?: string\n): { step: SetupStep; rulesPath: string | undefined } {\n  return {\n    step: { name: 'Rules File', status, message, durationMs: getTimeProvider().now() - startTime },\n    rulesPath,\n  };\n}\n\n/** Creates a hooks step result. */\nfunction makeHooksResult(\n  status: SetupStep['status'],\n  message: string,\n  startTime: number,\n  hookResult?: HookConfigResult\n): { step: SetupStep; hookSnippet: string | undefined; hookResult: HookConfigResult | undefined } {\n  return {\n    step: {\n      name: 'Hooks Configuration',\n      status,\n      message,\n      durationMs: getTimeProvider().now() - startTime,\n    },\n    hookSnippet: hookResult?.success === false ? generateHookSnippet() : undefined,\n    hookResult,\n  };\n}\n\n/**\n * Runs the rules file generation step.\n */\nfunction runRulesStep(\n  env: EnvironmentInfo,\n  options: SetupOptions\n): { step: SetupStep; rulesPath: string | undefined } {\n  const startTime = getTimeProvider().now();\n\n  if (options.skipRules) {\n    return makeRulesResult('skipped', 'Skipped (--skip-rules)', startTime);\n  }\n\n  const rulesPath = getRulesFilePath(env.projectInfo.root);\n  if (existsSync(rulesPath) && !options.force) {\n    return makeRulesResult(\n      'skipped',\n      'Rules file already exists (use --force to overwrite)',\n      startTime\n    );\n  }\n\n  try {\n    const createdPath = createRulesFile(env.projectInfo.root, options.dryRun);\n    const msg = options.dryRun ? `Would create: ${createdPath}` : `Created: ${createdPath}`;\n    return makeRulesResult('success', msg, startTime, createdPath);\n  } catch (error) {\n    const msg = getErrorMessage(error);\n    return makeRulesResult('failed', `Failed to create rules file: ${msg}`, startTime);\n  }\n}\n\n/**\n * Runs the hooks configuration step.\n * (Source: Issue #416 - Setup command hook configuration)\n */\nfunction runHooksStep(\n  env: EnvironmentInfo,\n  options: SetupOptions\n): { step: SetupStep; hookSnippet: string | undefined; hookResult: HookConfigResult | undefined } {\n  const startTime = getTimeProvider().now();\n\n  if (options.skipHooks) {\n    return makeHooksResult('skipped', 'Skipped (--skip-hooks)', startTime);\n  }\n\n  // If Claude CLI is not installed, we can't configure automatically\n  if (!env.claudeCli.installed) {\n    return makeHooksResult(\n      'warning',\n      'Claude CLI not found - manual hook configuration required',\n      startTime,\n      {\n        success: false,\n        alreadyConfigured: false,\n        message: 'Claude CLI not installed',\n      }\n    );\n  }\n\n  // If dry-run, just report what would happen\n  if (options.dryRun) {\n    return makeHooksResult(\n      'success',\n      'Would configure nexus-agents hooks in Claude Code settings',\n      startTime\n    );\n  }\n\n  // Configure using Claude CLI\n  const hookResult = configureHooks(options.force);\n  const status = hookResult.success\n    ? hookResult.alreadyConfigured\n      ? 'skipped'\n      : 'success'\n    : 'failed';\n\n  return makeHooksResult(status, hookResult.message, startTime, hookResult);\n}\n\n/**\n * Runs the OpenCode MCP configuration step (#1253).\n */\nfunction runOpenCodeStep(options: SetupOptions): SetupStep {\n  const startTime = getTimeProvider().now();\n  if (options.skipOpencode) {\n    return {\n      name: 'OpenCode MCP',\n      status: 'skipped',\n      message: 'Skipped (--skip-opencode)',\n      durationMs: 0,\n    };\n  }\n  const cliInfo = detectOpenCodeCli();\n  if (!cliInfo.installed) {\n    return {\n      name: 'OpenCode MCP',\n      status: 'skipped',\n      message: 'OpenCode CLI not installed',\n      durationMs: getTimeProvider().now() - startTime,\n    };\n  }\n  const result = configureOpenCode(options.force, options.dryRun);\n  return {\n    name: 'OpenCode MCP',\n    status: result.success ? (result.alreadyConfigured ? 'skipped' : 'success') : 'failed',\n    message: result.message,\n    durationMs: getTimeProvider().now() - startTime,\n  };\n}\n\n/**\n * Runs the Gemini CLI MCP configuration step (#1259).\n */\nfunction runGeminiStep(options: SetupOptions): SetupStep {\n  const startTime = getTimeProvider().now();\n  if (options.skipGemini) {\n    return {\n      name: 'Gemini MCP',\n      status: 'skipped',\n      message: 'Skipped (--skip-gemini)',\n      durationMs: 0,\n    };\n  }\n  const cliInfo = detectGeminiCli();\n  if (!cliInfo.installed) {\n    return {\n      name: 'Gemini MCP',\n      status: 'skipped',\n      message: 'Gemini CLI not installed',\n      durationMs: getTimeProvider().now() - startTime,\n    };\n  }\n  const result = configureGemini(options.force, options.dryRun, options.scope);\n  return {\n    name: 'Gemini MCP',\n    status: result.success ? (result.alreadyConfigured ? 'skipped' : 'success') : 'failed',\n    message: result.message,\n    durationMs: getTimeProvider().now() - startTime,\n  };\n}\n\n/**\n * Runs the data directory initialization step (#1249).\n */\nfunction runDataDirStep(options: SetupOptions): { step: SetupStep; result: DataDirInitResult } {\n  const startTime = getTimeProvider().now();\n  const dataDirResult = initDataDirectories(options.dryRun);\n  return {\n    step: {\n      name: 'Data Directory',\n      status: dataDirResult.success\n        ? dataDirResult.created.length > 0\n          ? 'success'\n          : 'skipped'\n        : 'failed',\n      message: dataDirResult.success\n        ? dataDirResult.created.length > 0\n          ? `Created ${String(dataDirResult.created.length)} directories`\n          : 'All directories already exist'\n        : `Failed: ${dataDirResult.error ?? 'Unknown error'}`,\n      durationMs: getTimeProvider().now() - startTime,\n    },\n    result: dataDirResult,\n  };\n}\n\n/**\n * Runs the Codex CLI MCP configuration step (#1263).\n */\nfunction runCodexStep(options: SetupOptions): SetupStep {\n  const startTime = getTimeProvider().now();\n  if (options.skipCodex) {\n    return {\n      name: 'Codex MCP',\n      status: 'skipped',\n      message: 'Skipped (--skip-codex)',\n      durationMs: 0,\n    };\n  }\n  const cliInfo = detectCodexCli();\n  if (!cliInfo.installed) {\n    return {\n      name: 'Codex MCP',\n      status: 'skipped',\n      message: 'Codex CLI not installed',\n      durationMs: getTimeProvider().now() - startTime,\n    };\n  }\n  const result = configureCodex(options.force, options.dryRun);\n  return {\n    name: 'Codex MCP',\n    status: result.success ? (result.alreadyConfigured ? 'skipped' : 'success') : 'failed',\n    message: result.message,\n    durationMs: getTimeProvider().now() - startTime,\n  };\n}\n\n/**\n * Runs the config file generation step (#1252).\n */\nfunction runConfigStep(projectRoot: string, options: SetupOptions): SetupStep {\n  const startTime = getTimeProvider().now();\n  if (options.skipConfig) {\n    return {\n      name: 'Configuration',\n      status: 'skipped',\n      message: 'Skipped (--skip-config)',\n      durationMs: 0,\n    };\n  }\n  const result = runConfigInitSync(projectRoot, options.force, options.dryRun);\n  return {\n    name: 'Configuration',\n    status: result.success ? (result.created ? 'success' : 'skipped') : 'failed',\n    message: result.message,\n    durationMs: getTimeProvider().now() - startTime,\n  };\n}\n\n/** Checks a named step's status, returning a check or issue string. */\nfunction checkStepStatus(steps: readonly SetupStep[], name: string, label: string): string {\n  const step = steps.find((s) => s.name === name);\n  const ok = step?.status === 'success' || step?.status === 'skipped';\n  return ok ? `${label} OK` : `${label} failed`;\n}\n\n/**\n * Runs post-setup validation step (#1271).\n * Checks that critical setup outcomes are in place.\n */\nfunction runValidationStep(steps: readonly SetupStep[]): SetupStep {\n  const startTime = getTimeProvider().now();\n\n  const mcpSteps = steps.filter((s) => s.name.includes('MCP'));\n  const mcpFailed = mcpSteps.filter((s) => s.status === 'failed').length;\n  const mcpCheck =\n    mcpFailed > 0\n      ? `${String(mcpFailed)} MCP config(s) failed`\n      : `${String(mcpSteps.length)} MCP configs OK`;\n\n  const results = [\n    mcpCheck,\n    checkStepStatus(steps, 'Data Directory', 'Data dirs'),\n    checkStepStatus(steps, 'Configuration', 'Config'),\n  ];\n  const hasIssues = results.some((r) => r.includes('failed'));\n\n  return {\n    name: 'Validation',\n    status: hasIssues ? 'warning' : 'success',\n    message: `${results.join(', ')}. Run \\`nexus-agents doctor\\` for full health check`,\n    durationMs: getTimeProvider().now() - startTime,\n  };\n}\n\n// ============================================================================\n// Main Command Helpers\n// ============================================================================\n\n/**\n * Adds Claude CLI warnings if not installed.\n */\nfunction addClaudeCliWarnings(warnings: string[], installed: boolean): void {\n  if (!installed) {\n    warnings.push(\n      'Claude CLI not found. Install it with: npm install -g @anthropic-ai/claude-code'\n    );\n    warnings.push('The MCP snippet uses npx to run nexus-agents (works without global install).');\n  }\n}\n\n/**\n * Collects errors from failed steps.\n */\nfunction collectErrors(steps: readonly SetupStep[]): string[] {\n  return steps.filter((s) => s.status === 'failed').map((s) => s.message ?? `${s.name} failed`);\n}\n\n/** Result context for building final result. */\ninterface SetupResultContext {\n  startTime: number;\n  steps: SetupStep[];\n  warnings: string[];\n  mcpResult: McpConfigResult | undefined;\n  snippet: string | undefined;\n  hookResult: HookConfigResult | undefined;\n  hookSnippet: string | undefined;\n  rulesPath: string | undefined;\n  dataDirResult?: DataDirInitResult;\n}\n\n/** Checks if a config result represents a new (non-existing) success. */\nfunction isNewSuccess(result: McpConfigResult | HookConfigResult | undefined): boolean {\n  return result?.success === true && !result.alreadyConfigured;\n}\n\n/** Builds the final setup result from context. */\nfunction buildSetupResult(ctx: SetupResultContext): SetupResult {\n  const errors = collectErrors(ctx.steps);\n  return {\n    success: errors.length === 0,\n    steps: ctx.steps,\n    warnings: ctx.warnings,\n    errors,\n    durationMs: getTimeProvider().now() - ctx.startTime,\n    ...(isNewSuccess(ctx.mcpResult) && { mcpConfigured: true }),\n    ...(ctx.snippet !== undefined && { mcpSnippet: ctx.snippet }),\n    ...(isNewSuccess(ctx.hookResult) && { hooksConfigured: true }),\n    ...(ctx.hookSnippet !== undefined && { hookSnippet: ctx.hookSnippet }),\n    ...(ctx.rulesPath !== undefined && { rulesPath: ctx.rulesPath }),\n    ...(ctx.dataDirResult !== undefined && {\n      dataDirPath: ctx.dataDirResult.rootPath,\n      dataDirsCreated: ctx.dataDirResult.created.length,\n    }),\n  };\n}\n\n// ============================================================================\n// Main Command\n// ============================================================================\n\n/**\n * Runs the setup command.\n */\nexport function runSetup(options: Partial<SetupOptions> = {}): SetupResult {\n  const startTime = getTimeProvider().now();\n  const parsedOptions = SetupOptionsSchema.parse(options);\n  const projectRoot = process.cwd();\n\n  const warnings: string[] = [];\n\n  // Step 1: Environment Detection\n  const { env, step: detectionStep } = runDetectionStep(projectRoot);\n  addClaudeCliWarnings(warnings, env.claudeCli.installed);\n\n  // Step 2: Prerequisite Validation\n  const { step: prereqStep, warnings: prereqWarnings } = runPrerequisiteStep();\n  warnings.push(...prereqWarnings);\n\n  // Step 3: MCP Configuration\n  const { step: mcpStep, snippet, mcpResult } = runMcpConfigStep(env, parsedOptions);\n\n  // Step 4: Rules File\n  const { step: rulesStep, rulesPath } = runRulesStep(env, parsedOptions);\n\n  // Step 5: Hooks Configuration (Issue #416)\n  const { step: hooksStep, hookSnippet, hookResult } = runHooksStep(env, parsedOptions);\n\n  // Step 6: Data Directory Initialization (#1249)\n  const { step: dataDirStep, result: dataDirResult } = runDataDirStep(parsedOptions);\n\n  // Step 7: OpenCode MCP Configuration (#1253)\n  const openCodeStep = runOpenCodeStep(parsedOptions);\n\n  // Step 8: Gemini MCP Configuration (#1259)\n  const geminiStep = runGeminiStep(parsedOptions);\n\n  // Step 9: Codex MCP Configuration (#1263)\n  const codexStep = runCodexStep(parsedOptions);\n\n  const configStep = runConfigStep(projectRoot, parsedOptions); // Step 10\n  const steps = [\n    detectionStep,\n    prereqStep,\n    mcpStep,\n    rulesStep,\n    hooksStep,\n    dataDirStep,\n    openCodeStep,\n    geminiStep,\n    codexStep,\n    configStep,\n  ];\n  steps.push(runValidationStep(steps)); // Step 11: Validation (#1271)\n\n  return buildSetupResult({\n    startTime,\n    steps,\n    warnings,\n    mcpResult,\n    snippet,\n    hookResult,\n    hookSnippet,\n    rulesPath,\n    dataDirResult,\n  });\n}\n\n/** Prints optional detail sections (MCP, hooks, rules, data dir). */\nfunction printDetailSections(result: SetupResult): void {\n  if (result.mcpSnippet !== undefined || result.mcpConfigured === true) {\n    const mcpResult: McpConfigResult =\n      result.mcpConfigured === true\n        ? {\n            success: true,\n            alreadyConfigured: false,\n            message: 'Added nexus-agents MCP server to Claude Code',\n          }\n        : { success: false, alreadyConfigured: false, message: 'Manual configuration required' };\n    printMcpResult(mcpResult, result.mcpSnippet);\n  }\n  if (result.hookSnippet !== undefined || result.hooksConfigured === true) {\n    const hookResult: HookConfigResult =\n      result.hooksConfigured === true\n        ? {\n            success: true,\n            alreadyConfigured: false,\n            message: 'Configured nexus-agents hooks in Claude Code settings',\n          }\n        : { success: false, alreadyConfigured: false, message: 'Manual configuration required' };\n    printHooksResult(hookResult, result.hookSnippet);\n  }\n  if (result.rulesPath !== undefined) printRulesFile(result.rulesPath);\n  if (result.dataDirPath !== undefined) printDataDirSection(result);\n  printPermissionsSuggestion();\n}\n\n/** Prints the Claude Code permissions suggestion (#1945). */\nfunction printPermissionsSuggestion(): void {\n  const snippet = generatePermissionsSnippet('all');\n  const banner = buildPermissionsBanner(snippet);\n  writeLine(banner);\n}\n\n/** Prints the data directory section. */\nfunction printDataDirSection(result: SetupResult): void {\n  writeLine(formatHeader('Data Directory'));\n  writeLine('─'.repeat(40));\n  const count = result.dataDirsCreated ?? 0;\n  const msg =\n    count > 0\n      ? `Created ${String(count)} directories under ${result.dataDirPath ?? ''}`\n      : `All directories already exist at ${result.dataDirPath ?? ''}`;\n  writeLine(msg);\n  writeEmptyLine();\n}\n\n/**\n * Prints the setup result.\n */\nexport function printSetupResult(result: SetupResult, verbose: boolean): void {\n  writeEmptyLine();\n  writeLine(formatHeader(`Nexus Agents Setup v${VERSION}`));\n  writeLine('═'.repeat(40));\n  writeEmptyLine();\n\n  printSteps(result.steps, verbose);\n  printDetailSections(result);\n\n  if (result.warnings.length > 0) printWarnings(result.warnings);\n  if (result.errors.length > 0) printErrors(result.errors);\n  printNextSteps(result.mcpConfigured === true, result.mcpSnippet !== undefined);\n  printSummary(result.success);\n}\n\n/**\n * Prints the post-setup \"Getting Started\" banner (#2138).\n *\n * Three numbered steps tailored to what setup actually configured. If Claude\n * Code's MCP wiring succeeded we point step 2 at the integrated harness\n * (`/mcp` in Claude); otherwise we suggest the standalone `orchestrate`\n * command. Always shown after a successful setup — printing 3 lines is not\n * worth gating on first-run detection.\n *\n * @param mcpConfigured - True when an MCP harness (Claude/etc.) was wired up.\n */\nfunction printGettingStartedBanner(mcpConfigured: boolean): void {\n  writeEmptyLine();\n  writeLine(formatHeader('Getting started'));\n  writeLine('─'.repeat(40));\n\n  writeLine('  1. nexus-agents hello             — guided tour (no API keys needed)');\n  if (mcpConfigured) {\n    writeLine('  2. Use through Claude Code        — type /mcp in Claude to list tools');\n  } else {\n    writeLine('  2. nexus-agents orchestrate \"...\"  — run your first task');\n  }\n  writeLine('  3. nexus-agents workflow list     — explore built-in workflows');\n\n  writeEmptyLine();\n  writeLine(`  ${colors.dim}Docs: https://github.com/williamzujkowski/nexus-agents${colors.reset}`);\n  writeLine(`  ${colors.dim}Harness wiring: docs/guides/HARNESS_COMPATIBILITY.md${colors.reset}`);\n}\n\n/**\n * Runs the post-setup health gate (#2137).\n *\n * After setup writes its files, this runs the verify checks and prints a\n * structured health summary inline. Returns `true` when no `severity: 'hard'`\n * checks failed — warnings still pass the gate.\n *\n * In `--dry-run` mode, the gate is skipped entirely (the user is previewing,\n * not actually installing).\n */\nasync function runPostSetupHealthGate(dryRun: boolean): Promise<boolean> {\n  if (dryRun) return true;\n\n  const result = await runVerify();\n  const passed = result.checks.filter((c) => c.passed).length;\n  const total = result.checks.length;\n\n  writeEmptyLine();\n  writeLine(formatHeader(`Health check (${String(passed)}/${String(total)} passed)`));\n  writeLine('─'.repeat(40));\n\n  for (const check of result.checks) {\n    let symbol: string;\n    if (check.passed) {\n      symbol = `${colors.green}${symbols.check}${colors.reset}`;\n    } else if (check.severity === 'warn') {\n      symbol = `${colors.yellow}${symbols.warn}${colors.reset}`;\n    } else {\n      symbol = `${colors.red}${symbols.cross}${colors.reset}`;\n    }\n    writeLine(`  ${symbol} ${check.name}: ${check.message}`);\n    if (!check.passed && check.fix !== undefined) {\n      writeLine(`     ${colors.dim}→ Fix: ${check.fix}${colors.reset}`);\n    }\n  }\n\n  writeEmptyLine();\n  if (!result.noHardFailures) {\n    writeLine(\n      `${colors.red}${colors.bold}Action required: fix the blocking issues above before using nexus-agents.${colors.reset}`\n    );\n  } else if (!result.allPassed) {\n    const warnCount = result.checks.filter((c) => !c.passed).length;\n    writeLine(\n      `${colors.yellow}${colors.bold}Setup complete with ${String(warnCount)} warning(s) — nexus-agents will run but some features are degraded.${colors.reset}`\n    );\n  } else {\n    writeLine(\n      `${colors.green}${colors.bold}All health checks passed. nexus-agents is ready.${colors.reset}`\n    );\n  }\n\n  return result.noHardFailures;\n}\n\n/**\n * Setup command entry point (synchronous, non-interactive).\n *\n * @returns Exit code (0 = success, 1 = failure)\n */\nexport function setupCommand(options: Partial<SetupOptions> = {}): number {\n  const parsedOptions = SetupOptionsSchema.parse(options);\n\n  // Check for non-interactive mode in CI\n  if (!isInteractive() && !parsedOptions.nonInteractive) {\n    writeLine('Non-interactive environment detected.');\n    writeLine('Run with --non-interactive or set CI=true.');\n    return 1;\n  }\n\n  const result = runSetup(options);\n  printSetupResult(result, parsedOptions.verbose);\n\n  return result.success ? 0 : 1;\n}\n\n/** Extended options including interactive flag. */\nexport interface SetupCommandOptions extends Partial<SetupOptions> {\n  interactive?: boolean;\n}\n\n/**\n * Setup command entry point with interactive wizard support.\n * (Source: Issue #425 - Interactive setup wizard)\n *\n * Also runs the post-setup health gate (#2137): after the configuration\n * steps complete, calls into `runVerify()` to surface install-time issues\n * that are easy to miss but break things at runtime (better-sqlite3 native\n * build, data dir writability, missing API keys). Health-gate warnings do\n * NOT fail setup — only `severity: 'hard'` failures do.\n *\n * @returns Exit code (0 = setup + no hard health failures, 1 = either failed)\n */\n/**\n * Runs the interactive wizard branch and returns its exit code.\n * Extracted from `setupCommandAsync` to keep cyclomatic complexity ≤10.\n */\nasync function runInteractiveSetup(options: SetupCommandOptions): Promise<number> {\n  const wizardOptions = await runWizard();\n  if (wizardOptions === undefined) return 1; // User cancelled.\n\n  const mergedOptions = { ...options, ...wizardOptions };\n  delete mergedOptions.interactive;\n\n  const result = runSetup(mergedOptions);\n  printSetupResult(result, mergedOptions.verbose ?? false);\n  const healthOk = await runPostSetupHealthGate(mergedOptions.dryRun ?? false);\n  if (result.success && !(mergedOptions.dryRun ?? false)) {\n    printGettingStartedBanner(result.mcpConfigured === true);\n  }\n  return result.success && healthOk ? 0 : 1;\n}\n\nexport async function setupCommandAsync(options: SetupCommandOptions = {}): Promise<number> {\n  if (options.interactive === true) {\n    return runInteractiveSetup(options);\n  }\n\n  // Sync setup, then run the health gate, then print the getting-started banner.\n  const setupResult = runSetupAndPrint(options);\n  const healthOk = await runPostSetupHealthGate(options.dryRun ?? false);\n  if (setupResult.exitCode === 0 && !(options.dryRun ?? false)) {\n    printGettingStartedBanner(setupResult.mcpConfigured);\n  }\n  // Hard health failures override a successful setup; warnings don't.\n  return setupResult.exitCode !== 0 || !healthOk ? 1 : 0;\n}\n\n/**\n * Runs setupCommand and captures both the exit code and the\n * `mcpConfigured` signal we need for the banner. Wraps the existing\n * synchronous path without changing its signature.\n */\nfunction runSetupAndPrint(options: SetupCommandOptions): {\n  exitCode: number;\n  mcpConfigured: boolean;\n} {\n  const parsedOptions = SetupOptionsSchema.parse(options);\n  if (!isInteractive() && !parsedOptions.nonInteractive) {\n    writeLine('Non-interactive environment detected.');\n    writeLine('Run with --non-interactive or set CI=true.');\n    return { exitCode: 1, mcpConfigured: false };\n  }\n  const result = runSetup(options);\n  printSetupResult(result, parsedOptions.verbose);\n  return { exitCode: result.success ? 0 : 1, mcpConfigured: result.mcpConfigured === true };\n}\n\n// ============================================================================\n// Exports\n// ============================================================================\n\nexport { generateMcpSnippet, generateRulesContent, detectEnvironment };\nexport { runWizard } from './setup-wizard.js';\nexport type { SetupOptions, SetupResult };\n// SetupCommandOptions is already exported via interface definition above\nexport type { WizardAnswers, UsageMode } from './setup-wizard.js';\n","/**\n * nexus-agents setup command types\n *\n * Type definitions for the user onboarding automation system.\n *\n * @module cli/setup-types\n * (Source: Issue #363 - Auto-configure Claude CLI integration)\n */\n\nimport { z } from 'zod';\nimport type { CommandResult } from '../core/index.js';\n\n/**\n * Setup command options schema.\n */\nexport const SetupOptionsSchema = z.object({\n  /** Skip interactive prompts */\n  nonInteractive: z.boolean().default(false),\n  /** Overwrite existing configurations */\n  force: z.boolean().default(false),\n  /** Skip MCP configuration */\n  skipMcp: z.boolean().default(false),\n  /** Skip CLAUDE.md/rules generation */\n  skipRules: z.boolean().default(false),\n  /** Skip hooks configuration (Issue #416) */\n  skipHooks: z.boolean().default(false),\n  /** Skip config file generation (#1252) */\n  skipConfig: z.boolean().default(false),\n  /** Skip OpenCode MCP configuration (#1253) */\n  skipOpencode: z.boolean().default(false),\n  /** Skip Gemini CLI MCP configuration (#1259) */\n  skipGemini: z.boolean().default(false),\n  /** Skip Codex CLI MCP configuration (#1263) */\n  skipCodex: z.boolean().default(false),\n  /** Show what would be done without making changes */\n  dryRun: z.boolean().default(false),\n  /** Show detailed output */\n  verbose: z.boolean().default(false),\n  /** Target scope for MCP config */\n  scope: z.enum(['user', 'project']).default('user'),\n});\n\nexport type SetupOptions = z.infer<typeof SetupOptionsSchema>;\n\n/**\n * Claude CLI detection result.\n */\nexport interface ClaudeCliInfo {\n  readonly installed: boolean;\n  readonly version: string | undefined;\n  readonly configPath: string;\n  readonly mcpJsonPath: string;\n}\n\n/**\n * Existing MCP configuration info.\n */\nexport interface McpConfigInfo {\n  readonly exists: boolean;\n  readonly path: string;\n  readonly hasNexusAgents: boolean;\n  readonly servers: readonly string[];\n}\n\n/**\n * MCP server configuration entry.\n */\nexport interface McpServerEntry {\n  readonly command: string;\n  readonly args?: readonly string[];\n  readonly env?: Record<string, string>;\n}\n\n/**\n * MCP JSON configuration format.\n */\nexport interface McpJsonConfig {\n  readonly mcpServers?: Record<string, McpServerEntry>;\n}\n\n/**\n * Project type detection.\n */\nexport type ProjectType =\n  | 'typescript'\n  | 'javascript'\n  | 'python'\n  | 'rust'\n  | 'go'\n  | 'java'\n  | 'unknown';\n\n/**\n * Project information.\n */\nexport interface ProjectInfo {\n  readonly root: string;\n  readonly hasPackageJson: boolean;\n  readonly hasClaudeMd: boolean;\n  readonly hasClaudeRules: boolean;\n  readonly hasNexusConfig: boolean;\n  readonly projectType: ProjectType;\n  readonly packageName?: string;\n}\n\n/**\n * Complete environment information.\n */\nexport interface EnvironmentInfo {\n  readonly platform: NodeJS.Platform;\n  readonly homeDir: string;\n  readonly claudeCli: ClaudeCliInfo;\n  readonly existingMcpConfig: McpConfigInfo | undefined;\n  readonly projectInfo: ProjectInfo;\n}\n\n/**\n * Setup step status.\n */\nexport interface SetupStep {\n  readonly name: string;\n  readonly status: 'pending' | 'success' | 'skipped' | 'failed' | 'warning';\n  readonly message?: string;\n  readonly durationMs?: number;\n}\n\n/**\n * Setup result summary.\n * Extends CommandResult base pattern (Issue #584).\n */\nexport interface SetupResult extends CommandResult {\n  /** Setup steps executed */\n  readonly steps: readonly SetupStep[];\n  /** MCP configuration was successful via Claude CLI */\n  readonly mcpConfigured?: boolean;\n  /** Fallback MCP snippet for manual configuration */\n  readonly mcpSnippet?: string;\n  /** Hooks configuration was successful via Claude CLI (Issue #416) */\n  readonly hooksConfigured?: boolean;\n  /** Fallback hook snippet for manual configuration */\n  readonly hookSnippet?: string;\n  readonly rulesPath?: string;\n  /** Data directory path if initialized (#1249) */\n  readonly dataDirPath?: string;\n  /** Number of data directories created (#1249) */\n  readonly dataDirsCreated?: number;\n  readonly warnings: readonly string[];\n  readonly errors: readonly string[];\n  readonly durationMs: number;\n}\n\n/**\n * Backup information for rollback.\n */\nexport interface BackupInfo {\n  readonly type: 'file';\n  readonly originalPath: string;\n  readonly backupPath: string;\n  readonly content: string;\n}\n\n/**\n * Rollback item types.\n */\nexport type RollbackItem =\n  | { type: 'file-backup'; backup: BackupInfo }\n  | { type: 'file-created'; path: string }\n  | { type: 'file-modified'; backup: BackupInfo };\n","/**\n * nexus-agents setup environment detection\n *\n * Environment detection helpers for Claude CLI and project setup.\n *\n * @module cli/setup-environment\n * (Source: Issue #363 - Auto-configure Claude CLI integration)\n */\n\nimport { execSync } from 'node:child_process';\nimport { existsSync, readFileSync } from 'node:fs';\nimport { homedir } from 'node:os';\nimport { join, basename } from 'node:path';\nimport { CLI_SUBPROCESS_TIMEOUTS } from '../config/timeouts.js';\nimport type {\n  ClaudeCliInfo,\n  McpConfigInfo,\n  ProjectInfo,\n  ProjectType,\n  EnvironmentInfo,\n} from './setup-types.js';\n\n/**\n * Parses Claude CLI version from output.\n */\nfunction parseClaudeVersion(output: string): string | undefined {\n  const match = output.match(/(\\d+\\.\\d+\\.\\d+)/);\n  return match?.[1];\n}\n\n/**\n * Detects if Claude CLI is installed and available.\n * Uses a 3-second timeout to avoid hanging in slow environments.\n */\nexport function detectClaudeCli(): ClaudeCliInfo {\n  const configPath = join(homedir(), '.claude');\n  const mcpJsonPath = join(homedir(), '.claude.json');\n\n  try {\n    const result = execSync('claude --version', {\n      encoding: 'utf-8',\n      stdio: ['pipe', 'pipe', 'pipe'],\n      timeout: CLI_SUBPROCESS_TIMEOUTS.envSetupMs,\n    });\n    const version = parseClaudeVersion(result);\n\n    return {\n      installed: true,\n      version,\n      configPath,\n      mcpJsonPath,\n    };\n  } catch {\n    return {\n      installed: false,\n      version: undefined,\n      configPath,\n      mcpJsonPath,\n    };\n  }\n}\n\n/** Extracts MCP servers from direct mcpServers key (project-scoped .mcp.json). */\nfunction extractDirectServers(config: Record<string, unknown>): string[] | undefined {\n  const mcpServers = config['mcpServers'] as Record<string, unknown> | undefined;\n  if (mcpServers === undefined) return undefined;\n  return Object.keys(mcpServers);\n}\n\n/** Extracts MCP servers from projects key (~/.claude.json format). */\nfunction extractProjectServers(config: Record<string, unknown>): string[] | undefined {\n  const projects = config['projects'] as Record<string, Record<string, unknown>> | undefined;\n  if (projects === undefined) return undefined;\n  const allServers = new Set<string>();\n  for (const proj of Object.values(projects)) {\n    const mcpServers = proj['mcpServers'] as Record<string, unknown> | undefined;\n    if (mcpServers !== undefined) Object.keys(mcpServers).forEach((n) => allServers.add(n));\n  }\n  return [...allServers];\n}\n\n/** Builds McpConfigInfo from a server list. */\nfunction buildMcpInfo(path: string, servers: string[]): McpConfigInfo {\n  return { exists: true, path, hasNexusAgents: servers.includes('nexus-agents'), servers };\n}\n\n/**\n * Detects existing MCP configuration.\n *\n * Handles two formats:\n * - `.mcp.json` (project-scoped): `{ mcpServers: { ... } }`\n * - `~/.claude.json` (user-scoped): `{ projects: { [path]: { mcpServers: { ... } } } }`\n */\nexport function detectMcpConfig(mcpJsonPath: string): McpConfigInfo | undefined {\n  if (!existsSync(mcpJsonPath)) return undefined;\n  try {\n    const config = JSON.parse(readFileSync(mcpJsonPath, 'utf-8')) as Record<string, unknown>;\n    const direct = extractDirectServers(config);\n    if (direct !== undefined) return buildMcpInfo(mcpJsonPath, direct);\n    const projected = extractProjectServers(config);\n    if (projected !== undefined) return buildMcpInfo(mcpJsonPath, projected);\n    return buildMcpInfo(mcpJsonPath, []);\n  } catch {\n    return buildMcpInfo(mcpJsonPath, []);\n  }\n}\n\n/** Checks for TypeScript in package.json devDependencies. */\nfunction hasTypeScriptInPackageJson(root: string): boolean {\n  try {\n    const content = readFileSync(join(root, 'package.json'), 'utf-8');\n    const parsed: unknown = JSON.parse(content);\n    const pkg = parsed as Record<string, unknown>;\n    const devDeps = pkg['devDependencies'] as Record<string, string> | undefined;\n    return devDeps?.['typescript'] !== undefined;\n  } catch {\n    return false;\n  }\n}\n\n/** Mapping of config files to project types. */\nconst CONFIG_FILE_TYPES: readonly [string, ProjectType][] = [\n  ['tsconfig.json', 'typescript'],\n  ['Cargo.toml', 'rust'],\n  ['go.mod', 'go'],\n  ['pyproject.toml', 'python'],\n  ['setup.py', 'python'],\n  ['pom.xml', 'java'],\n  ['build.gradle', 'java'],\n];\n\n/**\n * Detects project type based on configuration files.\n */\nexport function detectProjectType(root: string): ProjectType {\n  // Check config files\n  for (const [file, type] of CONFIG_FILE_TYPES) {\n    if (existsSync(join(root, file))) return type;\n  }\n\n  // Check package.json\n  if (existsSync(join(root, 'package.json'))) {\n    return hasTypeScriptInPackageJson(root) ? 'typescript' : 'javascript';\n  }\n\n  return 'unknown';\n}\n\n/**\n * Detects project information.\n */\nexport function detectProjectInfo(root: string): ProjectInfo {\n  let packageName: string | undefined;\n\n  if (existsSync(join(root, 'package.json'))) {\n    try {\n      const content = readFileSync(join(root, 'package.json'), 'utf-8');\n      const pkg = JSON.parse(content) as Record<string, unknown>;\n      const nameValue = pkg['name'];\n      packageName = typeof nameValue === 'string' ? nameValue : undefined;\n    } catch (parseErr: unknown) {\n      // Non-critical: package.json parse failure, fall through to basename\n      void parseErr;\n    }\n  }\n\n  return {\n    root,\n    hasPackageJson: existsSync(join(root, 'package.json')),\n    hasClaudeMd: existsSync(join(root, 'CLAUDE.md')),\n    // Rules relocated in #2121: canonical is `.rules/`. Still accept the\n    // legacy `.claude/rules/` path so detection doesn't break on repos that\n    // haven't migrated yet.\n    hasClaudeRules: existsSync(join(root, '.rules')) || existsSync(join(root, '.claude', 'rules')),\n    hasNexusConfig: existsSync(join(root, 'nexus-agents.yaml')),\n    projectType: detectProjectType(root),\n    packageName: packageName ?? basename(root),\n  };\n}\n\n/**\n * Detects complete environment information.\n */\nexport function detectEnvironment(projectRoot: string): EnvironmentInfo {\n  const claudeCli = detectClaudeCli();\n  const existingMcpConfig = detectMcpConfig(claudeCli.mcpJsonPath);\n  const projectInfo = detectProjectInfo(projectRoot);\n\n  return {\n    platform: process.platform,\n    homeDir: homedir(),\n    claudeCli,\n    existingMcpConfig,\n    projectInfo,\n  };\n}\n","/**\n * nexus-agents setup MCP configuration\n *\n * MCP configuration helpers using Claude CLI's `claude mcp` commands.\n *\n * @module cli/setup-mcp\n * (Source: Issue #363 - Auto-configure Claude CLI integration)\n */\n\nimport { execSync, execFileSync } from 'node:child_process';\nimport { homedir } from 'node:os';\nimport { join } from 'node:path';\nimport type { McpJsonConfig, McpServerEntry } from './setup-types.js';\nimport { getErrorMessage } from '../core/index.js';\n\n/** MCP entry for nexus-agents */\nexport const NEXUS_AGENTS_MCP_ENTRY: McpServerEntry = {\n  command: 'nexus-agents',\n  args: ['--mode=server'],\n};\n\n/** MCP entry with npx for users who install globally */\nexport const NEXUS_AGENTS_MCP_NPX_ENTRY: McpServerEntry = {\n  command: 'npx',\n  args: ['-y', 'nexus-agents@latest', '--mode=server'],\n};\n\n/**\n * Result of MCP configuration attempt.\n */\nexport interface McpConfigResult {\n  success: boolean;\n  alreadyConfigured: boolean;\n  message: string;\n}\n\n/**\n * Checks if nexus-agents MCP server is already configured in Claude CLI.\n */\nexport function isMcpServerConfigured(): boolean {\n  try {\n    const result = execSync('claude mcp get nexus-agents', {\n      encoding: 'utf-8',\n      stdio: ['pipe', 'pipe', 'pipe'],\n    });\n    return result.includes('nexus-agents');\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Maps scope option to Claude CLI `-s` flag value.\n */\nfunction scopeToFlag(scope: 'user' | 'project'): string {\n  return scope === 'project' ? 'local' : 'user';\n}\n\n/**\n * Removes existing MCP server configuration if present.\n */\nfunction removeExistingMcpServer(scope: 'user' | 'project' = 'user'): void {\n  try {\n    execSync(`claude mcp remove nexus-agents -s ${scopeToFlag(scope)}`, {\n      encoding: 'utf-8',\n      stdio: ['pipe', 'pipe', 'pipe'],\n    });\n  } catch {\n    // Ignore removal errors\n  }\n}\n\n/**\n * Adds MCP server to Claude CLI.\n */\nfunction addMcpServer(useNpx: boolean, scope: 'user' | 'project' = 'user'): McpConfigResult {\n  const entry = useNpx ? NEXUS_AGENTS_MCP_NPX_ENTRY : NEXUS_AGENTS_MCP_ENTRY;\n  const jsonConfig = JSON.stringify(entry);\n  const scopeLabel = scope === 'project' ? 'project' : 'global';\n\n  try {\n    execFileSync(\n      'claude',\n      ['mcp', 'add-json', 'nexus-agents', jsonConfig, '-s', scopeToFlag(scope)],\n      {\n        encoding: 'utf-8',\n        stdio: ['pipe', 'pipe', 'pipe'],\n      }\n    );\n    return {\n      success: true,\n      alreadyConfigured: false,\n      message: `Added nexus-agents MCP server to Claude Code (${scopeLabel})`,\n    };\n  } catch (error) {\n    const errorMsg = getErrorMessage(error);\n    return {\n      success: false,\n      alreadyConfigured: false,\n      message: `Failed to add MCP server: ${errorMsg}`,\n    };\n  }\n}\n\n/**\n * Configures nexus-agents MCP server using Claude CLI.\n *\n * Uses `claude mcp add-json` to register the server.\n * @param scope - 'user' for global (~/.claude/mcp.json), 'project' for local (.mcp.json)\n */\nexport function configureMcpServer(\n  useNpx: boolean = false,\n  force: boolean = false,\n  scope: 'user' | 'project' = 'user'\n): McpConfigResult {\n  const isConfigured = isMcpServerConfigured();\n\n  // Check if already configured\n  if (!force && isConfigured) {\n    return {\n      success: true,\n      alreadyConfigured: true,\n      message: 'nexus-agents MCP server already configured (use --force to reconfigure)',\n    };\n  }\n\n  // Remove existing if forcing\n  if (force && isConfigured) {\n    removeExistingMcpServer(scope);\n  }\n\n  return addMcpServer(useNpx, scope);\n}\n\n/**\n * Generates MCP configuration snippet for manual setup (fallback).\n */\nexport function generateMcpSnippet(useNpx: boolean = false): string {\n  const entry = useNpx ? NEXUS_AGENTS_MCP_NPX_ENTRY : NEXUS_AGENTS_MCP_ENTRY;\n  const config: McpJsonConfig = {\n    mcpServers: {\n      'nexus-agents': entry,\n    },\n  };\n\n  return JSON.stringify(config, null, 2);\n}\n\n/**\n * Generates the full MCP config path based on scope.\n *\n * Claude Code uses:\n * - Project scope: `.mcp.json` in project root\n * - User scope: `~/.claude.json` (stores MCP config under `projects` key)\n */\nexport function getMcpJsonPath(scope: 'user' | 'project', projectRoot: string): string {\n  if (scope === 'project') {\n    return join(projectRoot, '.mcp.json');\n  }\n  return join(homedir(), '.claude.json');\n}\n\n// ============================================================================\n// Hook Configuration (Issue #411, #416)\n// ============================================================================\n\n/**\n * Generates hook configuration for Claude CLI settings.json.\n * (Source: Issue #411 - Claude CLI Hook Integration)\n */\nexport function generateHookConfig(): HookSettingsConfig {\n  return {\n    hooks: {\n      SessionStart: [\n        {\n          hooks: [\n            {\n              type: 'command',\n              command: 'nexus-agents hooks session-start',\n            },\n          ],\n        },\n      ],\n      PreToolUse: [\n        {\n          matcher: 'Bash',\n          hooks: [\n            {\n              type: 'command',\n              command: 'nexus-agents hooks pre-tool --tool Bash --validate',\n            },\n          ],\n        },\n      ],\n      PostToolUse: [\n        {\n          matcher: '*',\n          hooks: [\n            {\n              type: 'command',\n              command: 'nexus-agents hooks post-tool --track-metrics',\n            },\n          ],\n        },\n      ],\n      Stop: [\n        {\n          hooks: [\n            {\n              type: 'command',\n              command: 'nexus-agents hooks stop --check-tasks',\n            },\n          ],\n        },\n      ],\n    },\n  };\n}\n\n/**\n * Hook command entry structure.\n */\ninterface HookCommandEntry {\n  type: 'command';\n  command: string;\n}\n\n/**\n * Hook matcher entry structure.\n */\ninterface HookMatcherEntry {\n  matcher?: string;\n  hooks: HookCommandEntry[];\n}\n\n/**\n * Hook settings configuration structure.\n */\nexport interface HookSettingsConfig {\n  hooks: {\n    SessionStart?: HookMatcherEntry[];\n    SessionEnd?: HookMatcherEntry[];\n    PreToolUse?: HookMatcherEntry[];\n    PostToolUse?: HookMatcherEntry[];\n    Stop?: HookMatcherEntry[];\n  };\n}\n\n/**\n * Result of hook configuration attempt.\n */\nexport interface HookConfigResult {\n  success: boolean;\n  alreadyConfigured: boolean;\n  message: string;\n}\n\n/**\n * Checks if hooks are already configured in Claude CLI settings.\n */\nexport function areHooksConfigured(): boolean {\n  try {\n    const result = execSync('claude config get hooks', {\n      encoding: 'utf-8',\n      stdio: ['pipe', 'pipe', 'pipe'],\n    });\n    // If we get output that includes nexus-agents, hooks are configured\n    return result.includes('nexus-agents');\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Reads existing hooks from Claude CLI settings.\n * Returns parsed hooks object or undefined if no hooks exist or parse fails.\n */\nexport function getExistingHooks(): HookSettingsConfig['hooks'] | undefined {\n  try {\n    const result = execSync('claude config get hooks', {\n      encoding: 'utf-8',\n      stdio: ['pipe', 'pipe', 'pipe'],\n    });\n    const trimmed = result.trim();\n    if (!trimmed || trimmed === 'null' || trimmed === 'undefined') {\n      return undefined;\n    }\n    return JSON.parse(trimmed) as HookSettingsConfig['hooks'];\n  } catch {\n    return undefined;\n  }\n}\n\n/**\n * Merges two hook arrays, combining entries without duplicating nexus-agents hooks.\n */\nfunction mergeHookArrays(\n  existing: HookMatcherEntry[] | undefined,\n  newHooks: HookMatcherEntry[]\n): HookMatcherEntry[] {\n  if (!existing || existing.length === 0) {\n    return newHooks;\n  }\n\n  // Filter out any existing nexus-agents hooks to avoid duplicates\n  const filteredExisting = existing.filter((entry) => {\n    return !entry.hooks.some((h) => h.command.startsWith('nexus-agents'));\n  });\n\n  // Combine existing (non-nexus) hooks with new nexus-agents hooks\n  return [...filteredExisting, ...newHooks];\n}\n\n/**\n * Merges nexus-agents hooks with existing hooks configuration.\n * Preserves existing user hooks while adding/updating nexus-agents hooks.\n */\nexport function mergeHookConfigs(\n  existing: HookSettingsConfig['hooks'] | undefined,\n  newConfig: HookSettingsConfig['hooks']\n): HookSettingsConfig['hooks'] {\n  if (!existing) {\n    return newConfig;\n  }\n\n  const hookTypes = ['SessionStart', 'SessionEnd', 'PreToolUse', 'PostToolUse', 'Stop'] as const;\n\n  const merged: HookSettingsConfig['hooks'] = {};\n\n  for (const hookType of hookTypes) {\n    const existingHooks = existing[hookType];\n    const newHooks = newConfig[hookType];\n\n    if (newHooks) {\n      merged[hookType] = mergeHookArrays(existingHooks, newHooks);\n    } else if (existingHooks) {\n      merged[hookType] = existingHooks;\n    }\n  }\n\n  return merged;\n}\n\n/**\n * Configures hooks in Claude CLI settings.\n * Uses `claude config set hooks` to register hook commands.\n * Merges with existing hooks instead of overwriting them (Issue #420).\n */\nexport function configureHooks(force: boolean = false): HookConfigResult {\n  const isConfigured = areHooksConfigured();\n\n  if (!force && isConfigured) {\n    return {\n      success: true,\n      alreadyConfigured: true,\n      message: 'Hooks already configured (use --force to reconfigure)',\n    };\n  }\n\n  const nexusHookConfig = generateHookConfig();\n\n  try {\n    // Read existing hooks first to merge (Issue #420)\n    const existingHooks = getExistingHooks();\n    const mergedHooks = mergeHookConfigs(existingHooks, nexusHookConfig.hooks);\n\n    // Use claude config set with merged hooks\n    const configJson = JSON.stringify(mergedHooks);\n    execFileSync('claude', ['config', 'set', 'hooks', configJson], {\n      encoding: 'utf-8',\n      stdio: ['pipe', 'pipe', 'pipe'],\n    });\n    return {\n      success: true,\n      alreadyConfigured: false,\n      message: existingHooks\n        ? 'Merged nexus-agents hooks with existing hooks in Claude Code settings'\n        : 'Configured nexus-agents hooks in Claude Code settings',\n    };\n  } catch (error) {\n    const errorMsg = getErrorMessage(error);\n    return {\n      success: false,\n      alreadyConfigured: false,\n      message: `Failed to configure hooks: ${errorMsg}`,\n    };\n  }\n}\n\n/**\n * Generates hook configuration snippet for manual setup.\n */\nexport function generateHookSnippet(): string {\n  const config = generateHookConfig();\n  return JSON.stringify(config, null, 2);\n}\n","/**\n * nexus-agents setup rules generation\n *\n * Rules file and backup management helpers.\n *\n * @module cli/setup-rules\n * (Source: Issue #363 - Auto-configure Claude CLI integration)\n */\n\nimport { readFileSync, writeFileSync, mkdirSync } from 'node:fs';\nimport { join, dirname } from 'node:path';\nimport { VERSION } from '../version.js';\nimport { getTimeProvider } from '../core/index.js';\nimport type { BackupInfo } from './setup-types.js';\n\n/**\n * Generates the nexus-agents rules file content.\n */\nexport function generateRulesContent(): string {\n  return `# Nexus-Agents Integration\n\nThis project uses [nexus-agents](https://github.com/williamzujkowski/nexus-agents) v${VERSION} for multi-agent orchestration.\n\n## MCP Tools Available\n\nWhen running with MCP server mode, these tools are available:\n\n| Tool | Description |\n| ---- | ----------- |\n| \\`orchestrate\\` | Task orchestration with Orchestrator coordination |\n| \\`create_expert\\` | Dynamic expert agent creation |\n| \\`run_workflow\\` | Execute workflow templates |\n| \\`delegate_to_model\\` | Route task to optimal model |\n| \\`list_experts\\` | List available expert types (discoverability) |\n| \\`list_workflows\\` | List available workflow templates |\n\n## Quick Commands\n\n\\`\\`\\`bash\n# Orchestrate a task with specialized experts\nnexus-agents orchestrate \"Implement feature X with tests\"\n\n# List available experts\nnexus-agents expert list\n\n# Run a workflow\nnexus-agents workflow list\nnexus-agents workflow run code-review --input='{\"url\": \"...\"}'\n\n# Check system health\nnexus-agents doctor\n\n# Generate config\nnexus-agents config init\n\\`\\`\\`\n\n## Usage Examples\n\n**Orchestrate a code review:**\n\\`\\`\\`\nUse nexus-agents to review this PR: https://github.com/owner/repo/pull/123\n\\`\\`\\`\n\n**Create a specialized expert:**\n\\`\\`\\`\nCreate a security expert to audit this codebase for vulnerabilities\n\\`\\`\\`\n\n**Run a workflow:**\n\\`\\`\\`\nRun the code-review workflow with the current changes\n\\`\\`\\`\n\n## Configuration\n\n- Config file: \\`./nexus-agents.yaml\\`\n- Generate config: \\`nexus-agents config init\\`\n- Check health: \\`nexus-agents doctor\\`\n\n---\n*Generated by nexus-agents setup v${VERSION}*\n`;\n}\n\n/**\n * Gets the rules file path.\n *\n * As of #2121 rules live at `<root>/.rules/` (harness-neutral location,\n * was `.claude/rules/`). Claude Code finds them via CLAUDE.md references,\n * so the move doesn't break its auto-load. Non-Claude harnesses (OpenCode,\n * Codex, Cursor, etc.) can point at the same directory.\n */\nexport function getRulesFilePath(projectRoot: string): string {\n  return join(projectRoot, '.rules', 'nexus-agents.md');\n}\n\n/**\n * Creates the rules file.\n */\nexport function createRulesFile(projectRoot: string, dryRun: boolean): string {\n  const rulesPath = getRulesFilePath(projectRoot);\n  const content = generateRulesContent();\n\n  if (!dryRun) {\n    const rulesDir = dirname(rulesPath);\n    mkdirSync(rulesDir, { recursive: true });\n    writeFileSync(rulesPath, content, 'utf-8');\n  }\n\n  return rulesPath;\n}\n\n/**\n * Creates a backup of a file.\n */\nexport function backupFile(filePath: string): BackupInfo {\n  const content = readFileSync(filePath, 'utf-8');\n  const backupPath = `${filePath}.backup.${String(getTimeProvider().now())}`;\n  writeFileSync(backupPath, content, 'utf-8');\n\n  return {\n    type: 'file',\n    originalPath: filePath,\n    backupPath,\n    content,\n  };\n}\n\n/**\n * Restores a file from backup.\n */\nexport function restoreBackup(backup: BackupInfo): void {\n  writeFileSync(backup.originalPath, backup.content, 'utf-8');\n}\n","/**\n * nexus-agents setup output formatting\n *\n * Output formatting helpers for setup command.\n * Re-exports from consolidated ansi-output.ts for backward compatibility.\n *\n * @module cli/setup-formatting\n * (Source: Issue #363 - Auto-configure Claude CLI integration)\n */\n\n// Re-export consolidated formatters from ansi-output.ts\nexport { formatStatus, formatHeader, formatCodeBlock, colors, symbols } from './ansi-output.js';\n\n/**\n * Checks if running in interactive mode.\n */\nexport function isInteractive(): boolean {\n  if (!process.stdout.isTTY) return false;\n  if (process.env['CI'] === 'true') return false;\n  if (process.env['CONTINUOUS_INTEGRATION'] !== undefined) return false;\n  return true;\n}\n","/**\n * OpenCode MCP auto-configuration for setup command.\n *\n * Detects OpenCode CLI and generates opencode.json/.jsonc with nexus-agents MCP server.\n * Supports JSONC (JSON with Comments) via `jsonc-parser` for comment-preserving writes.\n *\n * @module cli/setup-opencode\n * (Source: Issue #1253 - OpenCode MCP auto-configuration, #1255 - JSONC support)\n */\n\nimport { existsSync, readFileSync, writeFileSync, mkdirSync } from 'node:fs';\nimport { execFileSync } from 'node:child_process';\nimport { join, resolve } from 'node:path';\nimport { homedir, platform } from 'node:os';\nimport { parse as jsoncParse, modify, applyEdits } from 'jsonc-parser';\nimport { getErrorMessage } from '../core/index.js';\nimport { createLogger } from '../core/index.js';\n\nconst logger = createLogger({ component: 'setup-opencode' });\n\n/** OpenCode detection result. */\nexport interface OpenCodeCliInfo {\n  readonly installed: boolean;\n  readonly version: string | undefined;\n}\n\n/** OpenCode MCP configuration result. */\nexport interface OpenCodeConfigResult {\n  readonly success: boolean;\n  readonly alreadyConfigured: boolean;\n  readonly message: string;\n  readonly configPath: string;\n}\n\n/** Resolved config file info. */\nexport interface ResolvedConfig {\n  readonly path: string;\n  readonly isJsonc: boolean;\n  readonly exists: boolean;\n}\n\n/**\n * Detects OpenCode CLI installation.\n */\nexport function detectOpenCodeCli(): OpenCodeCliInfo {\n  try {\n    const cmd = platform() === 'win32' ? 'where' : 'which';\n    execFileSync(cmd, ['opencode'], { timeout: 3000, stdio: 'pipe' });\n  } catch {\n    return { installed: false, version: undefined };\n  }\n\n  try {\n    const output = execFileSync('opencode', ['--version'], {\n      timeout: 5000,\n      stdio: 'pipe',\n      encoding: 'utf-8',\n    });\n    const match = /(\\d+\\.\\d+\\.\\d+)/.exec(output);\n    return { installed: true, version: match?.[1] };\n  } catch {\n    return { installed: true, version: undefined };\n  }\n}\n\n/**\n * Resolves the OpenCode config directory path.\n * OpenCode uses ~/.config/opencode/ on Linux/macOS.\n */\nfunction getOpenCodeConfigDir(): string {\n  return join(homedir(), '.config', 'opencode');\n}\n\n/**\n * Resolves the path for nexus-agents CLI command.\n * Uses `npx nexus-agents` for portability.\n */\nfunction getNexusCommand(): readonly string[] {\n  return ['npx', 'nexus-agents', '--mode=server'];\n}\n\nconst NEXUS_MCP_ENTRY = {\n  type: 'local',\n  command: getNexusCommand(),\n  enabled: true,\n};\n\n/**\n * Resolves the OpenCode config file in a directory.\n * Prefers .jsonc over .json (matching OpenCode's own priority).\n */\nexport function resolveOpenCodeConfig(dir: string): ResolvedConfig {\n  const jsoncPath = join(dir, 'opencode.jsonc');\n  if (existsSync(jsoncPath)) {\n    return { path: jsoncPath, isJsonc: true, exists: true };\n  }\n  const jsonPath = join(dir, 'opencode.json');\n  if (existsSync(jsonPath)) {\n    return { path: jsonPath, isJsonc: false, exists: true };\n  }\n  return { path: jsonPath, isJsonc: false, exists: false };\n}\n\n/** Checks if nexus-agents is already configured in an existing config. */\nfunction isAlreadyConfigured(resolved: ResolvedConfig): boolean {\n  if (!resolved.exists) return false;\n  try {\n    const raw = readFileSync(resolved.path, 'utf-8');\n    const config = jsoncParse(raw) as Record<string, unknown> | null;\n    const mcp = config?.['mcp'] as Record<string, unknown> | undefined;\n    return mcp?.['nexus-agents'] !== undefined;\n  } catch {\n    logger.debug('Failed to parse existing OpenCode config, will overwrite');\n    return false;\n  }\n}\n\n/** Writes nexus-agents MCP entry using comment-preserving edits for JSONC. */\nfunction writeJsoncConfig(configPath: string, raw: string): void {\n  let result = raw;\n  result = applyEdits(result, modify(result, ['mcp', 'nexus-agents'], NEXUS_MCP_ENTRY, {}));\n  result = applyEdits(result, modify(result, ['$schema'], 'https://opencode.ai/config.json', {}));\n  writeFileSync(configPath, result, 'utf-8');\n}\n\n/** Writes nexus-agents MCP entry as plain JSON for new configs. */\nfunction writeJsonConfig(configPath: string): void {\n  const config = {\n    $schema: 'https://opencode.ai/config.json',\n    mcp: { 'nexus-agents': NEXUS_MCP_ENTRY },\n  };\n  writeFileSync(configPath, JSON.stringify(config, null, 2) + '\\n', 'utf-8');\n}\n\n/** Writes the merged config with nexus-agents MCP entry. */\nfunction writeOpenCodeConfig(configDir: string, resolved: ResolvedConfig): void {\n  if (!existsSync(configDir)) mkdirSync(configDir, { recursive: true });\n\n  if (resolved.exists) {\n    const raw = readFileSync(resolved.path, 'utf-8');\n    writeJsoncConfig(resolved.path, raw);\n  } else {\n    writeJsonConfig(resolved.path);\n  }\n}\n\n/** Options for configureOpenCode. */\nexport interface ConfigureOpenCodeOptions {\n  readonly force: boolean;\n  readonly dryRun: boolean;\n  readonly projectRoot?: string;\n}\n\n/** Validates projectRoot to prevent path traversal (CWE-22). */\nfunction validateProjectRoot(projectRoot: string): string {\n  const resolved = resolve(projectRoot);\n  if (!existsSync(resolved)) {\n    throw new Error(`Project root does not exist: ${resolved}`);\n  }\n  return resolved;\n}\n\n/**\n * Configures OpenCode with nexus-agents MCP server.\n * Supports both global (~/.config/opencode/) and project-local configs.\n */\nexport function configureOpenCode(\n  force: boolean,\n  dryRun: boolean,\n  options?: ConfigureOpenCodeOptions\n): OpenCodeConfigResult {\n  try {\n    return configureOpenCodeInner(force, dryRun, options);\n  } catch (error: unknown) {\n    const fallbackPath = join(getOpenCodeConfigDir(), 'opencode.json');\n    return {\n      success: false,\n      alreadyConfigured: false,\n      message: `Failed to configure OpenCode: ${getErrorMessage(error)}`,\n      configPath: fallbackPath,\n    };\n  }\n}\n\nfunction configureOpenCodeInner(\n  force: boolean,\n  dryRun: boolean,\n  options?: ConfigureOpenCodeOptions\n): OpenCodeConfigResult {\n  const configDir =\n    options?.projectRoot !== undefined\n      ? validateProjectRoot(options.projectRoot)\n      : getOpenCodeConfigDir();\n  const resolved = resolveOpenCodeConfig(configDir);\n\n  if (isAlreadyConfigured(resolved) && !force) {\n    return {\n      success: true,\n      alreadyConfigured: true,\n      message: 'nexus-agents already configured in OpenCode',\n      configPath: resolved.path,\n    };\n  }\n  if (dryRun) {\n    return {\n      success: true,\n      alreadyConfigured: false,\n      message: `Would configure nexus-agents MCP in ${resolved.path}`,\n      configPath: resolved.path,\n    };\n  }\n  writeOpenCodeConfig(configDir, resolved);\n  return {\n    success: true,\n    alreadyConfigured: false,\n    message: 'Configured nexus-agents MCP in OpenCode',\n    configPath: resolved.path,\n  };\n}\n","/**\n * Gemini CLI MCP auto-configuration for setup command.\n *\n * Detects Gemini CLI and configures ~/.gemini/settings.json with nexus-agents MCP server.\n *\n * @module cli/setup-gemini\n * (Source: Issue #1259 - Gemini CLI MCP auto-configuration)\n */\n\nimport { existsSync, readFileSync, writeFileSync, mkdirSync } from 'node:fs';\nimport { execFileSync } from 'node:child_process';\nimport { join } from 'node:path';\nimport { homedir, platform } from 'node:os';\nimport { getErrorMessage } from '../core/index.js';\nimport { createLogger } from '../core/index.js';\n\nconst logger = createLogger({ component: 'setup-gemini' });\n\n/** Gemini CLI detection result. */\nexport interface GeminiCliInfo {\n  readonly installed: boolean;\n  readonly version: string | undefined;\n}\n\n/** Gemini MCP configuration result. */\nexport interface GeminiConfigResult {\n  readonly success: boolean;\n  readonly alreadyConfigured: boolean;\n  readonly message: string;\n  readonly configPath: string;\n}\n\n/** Gemini MCP server entry format. */\ninterface GeminiMcpEntry {\n  readonly command: string;\n  readonly args: readonly string[];\n  readonly timeout: number;\n}\n\n/**\n * Detects Gemini CLI installation.\n */\nexport function detectGeminiCli(): GeminiCliInfo {\n  try {\n    const cmd = platform() === 'win32' ? 'where' : 'which';\n    execFileSync(cmd, ['gemini'], { timeout: 3000, stdio: 'pipe' });\n  } catch {\n    return { installed: false, version: undefined };\n  }\n\n  try {\n    const output = execFileSync('gemini', ['--version'], {\n      timeout: 5000,\n      stdio: 'pipe',\n      encoding: 'utf-8',\n    });\n    const match = /(\\d+\\.\\d+\\.\\d+)/.exec(output);\n    return { installed: true, version: match?.[1] };\n  } catch {\n    return { installed: true, version: undefined };\n  }\n}\n\n/** Resolves the Gemini config directory path based on scope. */\nfunction getGeminiConfigDir(scope: 'user' | 'project', projectRoot?: string): string {\n  if (scope === 'project' && projectRoot !== undefined) {\n    return join(projectRoot, '.gemini');\n  }\n  return join(homedir(), '.gemini');\n}\n\n/** Returns the nexus-agents MCP entry for Gemini settings.json. */\nfunction getNexusMcpEntry(): GeminiMcpEntry {\n  return {\n    command: 'npx',\n    args: ['nexus-agents', '--mode=server'],\n    timeout: 30000,\n  };\n}\n\n/** Checks if nexus-agents is already configured in settings.json. */\nfunction isAlreadyConfigured(configPath: string): boolean {\n  if (!existsSync(configPath)) return false;\n  try {\n    const config = JSON.parse(readFileSync(configPath, 'utf-8')) as Record<string, unknown>;\n    const servers = config['mcpServers'] as Record<string, unknown> | undefined;\n    return servers?.['nexus-agents'] !== undefined;\n  } catch {\n    logger.debug('Failed to parse existing Gemini settings.json, will overwrite');\n    return false;\n  }\n}\n\n/** Reads existing config or returns empty object. */\nfunction readExistingConfig(configPath: string): Record<string, unknown> {\n  if (!existsSync(configPath)) return {};\n  try {\n    return JSON.parse(readFileSync(configPath, 'utf-8')) as Record<string, unknown>;\n  } catch {\n    return {};\n  }\n}\n\n/** Writes the merged config with nexus-agents MCP entry. */\nfunction writeGeminiConfig(configDir: string, configPath: string): void {\n  if (!existsSync(configDir)) mkdirSync(configDir, { recursive: true });\n  const config = readExistingConfig(configPath);\n  const servers = (config['mcpServers'] ?? {}) as Record<string, unknown>;\n  servers['nexus-agents'] = getNexusMcpEntry();\n  config['mcpServers'] = servers;\n  writeFileSync(configPath, JSON.stringify(config, null, 2) + '\\n', 'utf-8');\n}\n\n/**\n * Configures Gemini CLI with nexus-agents MCP server.\n *\n * @param force - Force reconfiguration even if already configured\n * @param dryRun - Preview changes without writing\n * @param scope - 'user' for global (~/.gemini/), 'project' for project-local (.gemini/)\n * @param projectRoot - Project root directory (required for project scope)\n */\nexport function configureGemini(\n  force: boolean,\n  dryRun: boolean,\n  scope: 'user' | 'project' = 'user',\n  projectRoot?: string\n): GeminiConfigResult {\n  const configDir = getGeminiConfigDir(scope, projectRoot);\n  const configPath = join(configDir, 'settings.json');\n\n  if (isAlreadyConfigured(configPath) && !force) {\n    return {\n      success: true,\n      alreadyConfigured: true,\n      message: 'nexus-agents already configured in Gemini CLI',\n      configPath,\n    };\n  }\n  if (dryRun) {\n    return {\n      success: true,\n      alreadyConfigured: false,\n      message: `Would configure nexus-agents MCP in ${configPath}`,\n      configPath,\n    };\n  }\n  try {\n    writeGeminiConfig(configDir, configPath);\n    return {\n      success: true,\n      alreadyConfigured: false,\n      message: 'Configured nexus-agents MCP in Gemini CLI',\n      configPath,\n    };\n  } catch (error: unknown) {\n    return {\n      success: false,\n      alreadyConfigured: false,\n      message: `Failed to configure Gemini: ${getErrorMessage(error)}`,\n      configPath,\n    };\n  }\n}\n","/**\n * Codex CLI MCP auto-configuration for setup command.\n *\n * Detects Codex CLI and registers nexus-agents MCP server\n * using `codex mcp add` CLI command.\n *\n * @module cli/setup-codex\n * (Source: Issue #1263 - Codex CLI MCP auto-configuration)\n */\n\nimport { execFileSync } from 'node:child_process';\nimport { platform } from 'node:os';\nimport { getErrorMessage } from '../core/index.js';\nimport { createLogger } from '../core/index.js';\n\nconst logger = createLogger({ component: 'setup-codex' });\n\n/** Codex CLI detection result. */\nexport interface CodexCliInfo {\n  readonly installed: boolean;\n  readonly version: string | undefined;\n}\n\n/** Codex MCP configuration result. */\nexport interface CodexConfigResult {\n  readonly success: boolean;\n  readonly alreadyConfigured: boolean;\n  readonly message: string;\n}\n\n/**\n * Detects Codex CLI installation.\n */\nexport function detectCodexCli(): CodexCliInfo {\n  try {\n    const cmd = platform() === 'win32' ? 'where' : 'which';\n    execFileSync(cmd, ['codex'], { timeout: 3000, stdio: 'pipe' });\n  } catch {\n    return { installed: false, version: undefined };\n  }\n\n  try {\n    const output = execFileSync('codex', ['--version'], {\n      timeout: 5000,\n      stdio: 'pipe',\n      encoding: 'utf-8',\n    });\n    const match = /(\\d+\\.\\d+\\.\\d+)/.exec(output);\n    return { installed: true, version: match?.[1] };\n  } catch {\n    return { installed: true, version: undefined };\n  }\n}\n\n/**\n * Checks if nexus-agents is already configured in Codex MCP.\n */\nfunction isAlreadyConfigured(): boolean {\n  try {\n    const output = execFileSync('codex', ['mcp', 'list'], {\n      timeout: 5000,\n      stdio: 'pipe',\n      encoding: 'utf-8',\n    });\n    return output.includes('nexus-agents');\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Removes existing nexus-agents MCP configuration from Codex.\n */\nfunction removeExisting(): void {\n  try {\n    execFileSync('codex', ['mcp', 'remove', 'nexus-agents'], {\n      timeout: 5000,\n      stdio: 'pipe',\n    });\n  } catch {\n    logger.debug('Failed to remove existing Codex MCP config (may not exist)');\n  }\n}\n\n/**\n * Adds nexus-agents MCP server to Codex CLI.\n *\n * Uses: codex mcp add nexus-agents -- npx nexus-agents --mode=server\n */\nfunction addMcpServer(): CodexConfigResult {\n  try {\n    execFileSync(\n      'codex',\n      ['mcp', 'add', 'nexus-agents', '--', 'npx', 'nexus-agents', '--mode=server'],\n      {\n        timeout: 10000,\n        stdio: 'pipe',\n      }\n    );\n    return {\n      success: true,\n      alreadyConfigured: false,\n      message: 'Configured nexus-agents MCP in Codex CLI',\n    };\n  } catch (error: unknown) {\n    return {\n      success: false,\n      alreadyConfigured: false,\n      message: `Failed to configure Codex: ${getErrorMessage(error)}`,\n    };\n  }\n}\n\n/**\n * Configures Codex CLI with nexus-agents MCP server.\n */\nexport function configureCodex(force: boolean, dryRun: boolean): CodexConfigResult {\n  if (isAlreadyConfigured() && !force) {\n    return {\n      success: true,\n      alreadyConfigured: true,\n      message: 'nexus-agents already configured in Codex CLI',\n    };\n  }\n\n  if (dryRun) {\n    return {\n      success: true,\n      alreadyConfigured: false,\n      message: 'Would configure nexus-agents MCP in Codex CLI',\n    };\n  }\n\n  if (force && isAlreadyConfigured()) {\n    removeExisting();\n  }\n\n  return addMcpServer();\n}\n","/**\n * nexus-agents setup interactive wizard\n *\n * Guided setup experience for configuring nexus-agents with Claude CLI.\n * Uses Node.js readline for terminal prompts without external dependencies.\n *\n * @module cli/setup-wizard\n * (Source: Issue #425 - Interactive setup wizard)\n */\n\nimport { createInterface, type Interface } from 'node:readline';\nimport { formatHeader, formatStatus, isInteractive } from './setup-formatting.js';\nimport type { SetupOptions } from './setup-types.js';\n\n// ============================================================================\n// Types\n// ============================================================================\n\n/** Usage mode selection. */\nexport type UsageMode = 'claude-desktop' | 'claude-cli' | 'standalone' | 'all';\n\n/** Wizard answers collected from user. */\nexport interface WizardAnswers {\n  usageMode: UsageMode;\n  hasApiKeys: boolean;\n  configDirectory: string;\n  confirmProceed: boolean;\n}\n\n/** Wizard state during execution. */\ninterface WizardState {\n  currentStep: number;\n  totalSteps: number;\n  answers: Partial<WizardAnswers>;\n}\n\n// ============================================================================\n// Readline Helpers\n// ============================================================================\n\n/**\n * Creates a readline interface for prompting.\n */\nfunction createReadline(): Interface {\n  return createInterface({\n    input: process.stdin,\n    output: process.stdout,\n  });\n}\n\n/**\n * Prompts for input and returns the answer.\n */\nasync function promptInput(rl: Interface, question: string): Promise<string> {\n  return new Promise((resolve) => {\n    rl.question(question, (answer) => {\n      resolve(answer.trim());\n    });\n  });\n}\n\n/**\n * Prompts for a yes/no confirmation.\n */\nasync function promptConfirm(\n  rl: Interface,\n  question: string,\n  defaultValue = true\n): Promise<boolean> {\n  const defaultHint = defaultValue ? '[Y/n]' : '[y/N]';\n  const answer = await promptInput(rl, `${question} ${defaultHint}: `);\n\n  if (answer === '') return defaultValue;\n  return answer.toLowerCase().startsWith('y');\n}\n\n/**\n * Prints options for selection prompt.\n */\nfunction printOptions(\n  options: readonly { value: string; label: string }[],\n  defaultIndex: number\n): void {\n  for (let i = 0; i < options.length; i++) {\n    const option = options[i];\n    const marker = i === defaultIndex ? '>' : ' ';\n    const label = option?.label ?? '';\n    writeLine(`  ${marker} ${String(i + 1)}. ${label}`);\n  }\n}\n\n/**\n * Gets value from options at index with fallback.\n */\nfunction getOptionValue(\n  options: readonly { value: string; label: string }[],\n  index: number,\n  fallbackIndex: number\n): string {\n  const option = options[index];\n  if (option !== undefined) {\n    return option.value;\n  }\n  const fallback = options[fallbackIndex];\n  return fallback?.value ?? '';\n}\n\n/**\n * Prompts for a selection from a list of options.\n */\nasync function promptSelect(\n  rl: Interface,\n  question: string,\n  options: readonly { value: string; label: string }[],\n  defaultIndex = 0\n): Promise<string> {\n  writeLine('\\n' + question);\n  printOptions(options, defaultIndex);\n\n  const answer = await promptInput(rl, `\\nChoice [1-${String(options.length)}]: `);\n\n  if (answer === '') {\n    return getOptionValue(options, defaultIndex, 0);\n  }\n\n  const index = parseInt(answer, 10) - 1;\n  if (index >= 0 && index < options.length) {\n    return getOptionValue(options, index, 0);\n  }\n\n  return getOptionValue(options, defaultIndex, 0);\n}\n\n// ============================================================================\n// Output Helpers\n// ============================================================================\n\n/** Writes a line to stdout. */\nfunction writeLine(text: string): void {\n  process.stdout.write(text + '\\n');\n}\n\n/** Writes an empty line. */\nfunction writeEmptyLine(): void {\n  process.stdout.write('\\n');\n}\n\n/** Prints the wizard header. */\nfunction printWizardHeader(): void {\n  writeEmptyLine();\n  writeLine(formatHeader('Nexus Agents Setup Wizard'));\n  writeLine('='.repeat(40));\n  writeLine('This wizard will help you configure nexus-agents.');\n  writeEmptyLine();\n}\n\n/** Prints step progress. */\nfunction printStepProgress(state: WizardState, stepName: string): void {\n  writeLine(\n    `\\n${formatHeader(`Step ${String(state.currentStep)}/${String(state.totalSteps)}: ${stepName}`)}`\n  );\n  writeLine('-'.repeat(40));\n}\n\n/** Prints completion message. */\nfunction printCompletion(): void {\n  writeEmptyLine();\n  writeLine(formatStatus('success') + ' Wizard completed! Running setup...');\n  writeEmptyLine();\n}\n\n// ============================================================================\n// Wizard Steps\n// ============================================================================\n\n/** Usage mode options. */\nconst USAGE_MODE_OPTIONS: readonly { value: UsageMode; label: string }[] = [\n  { value: 'claude-cli', label: 'Claude CLI (terminal-based development)' },\n  { value: 'claude-desktop', label: 'Claude Desktop (GUI application)' },\n  { value: 'standalone', label: 'Standalone CLI (without Claude integration)' },\n  { value: 'all', label: 'All of the above' },\n];\n\n/**\n * Step 1: Ask how the user plans to use nexus-agents.\n */\nasync function askUsageMode(rl: Interface, state: WizardState): Promise<UsageMode> {\n  printStepProgress(state, 'Usage Mode');\n  writeLine('How will you use nexus-agents?');\n\n  const answer = await promptSelect(rl, '', USAGE_MODE_OPTIONS, 0);\n\n  return answer as UsageMode;\n}\n\n/**\n * Step 2: Ask about API key configuration.\n */\nasync function askApiKeys(rl: Interface, state: WizardState): Promise<boolean> {\n  printStepProgress(state, 'API Keys');\n  writeLine('nexus-agents works best with API keys configured.');\n  writeLine('Supported providers: Anthropic (Claude), OpenAI, Google (Gemini)');\n  writeEmptyLine();\n\n  const hasKeys = await promptConfirm(rl, 'Do you have at least one API key configured?', false);\n\n  if (!hasKeys) {\n    writeEmptyLine();\n    writeLine('No worries! You can configure API keys later:');\n    writeLine('  - ANTHROPIC_API_KEY for Claude');\n    writeLine('  - OPENAI_API_KEY for OpenAI/Codex');\n    writeLine('  - GOOGLE_AI_API_KEY for Gemini');\n    writeLine('\\nRun `nexus-agents doctor` to check your configuration.');\n  }\n\n  return hasKeys;\n}\n\n/**\n * Step 3: Ask about configuration directory.\n */\nasync function askConfigDirectory(rl: Interface, state: WizardState): Promise<string> {\n  printStepProgress(state, 'Configuration');\n  writeLine('Where should nexus-agents store its configuration?');\n  writeEmptyLine();\n\n  const defaultDir = process.cwd();\n  const answer = await promptInput(rl, `Directory [${defaultDir}]: `);\n\n  return answer || defaultDir;\n}\n\n/**\n * Step 4: Confirm and proceed.\n */\nasync function askConfirmation(\n  rl: Interface,\n  state: WizardState,\n  answers: Partial<WizardAnswers>\n): Promise<boolean> {\n  printStepProgress(state, 'Confirmation');\n  writeLine('Setup will configure the following:');\n  writeEmptyLine();\n\n  const modeLabel =\n    USAGE_MODE_OPTIONS.find((o) => o.value === answers.usageMode)?.label ?? 'Unknown';\n  const apiKeyStatus = answers.hasApiKeys === true ? 'Configured' : 'Not yet configured';\n  const configDir = answers.configDirectory ?? process.cwd();\n  writeLine(`  Usage mode: ${modeLabel}`);\n  writeLine(`  API keys: ${apiKeyStatus}`);\n  writeLine(`  Config directory: ${configDir}`);\n  writeEmptyLine();\n\n  const skipMcp = answers.usageMode === 'standalone';\n  if (!skipMcp) {\n    writeLine('Will configure:');\n    writeLine('  - MCP server for Claude integration');\n    writeLine('  - Rules file (.rules/nexus-agents.md)');\n    writeLine('  - Hooks for session tracking');\n  } else {\n    writeLine('Will configure:');\n    writeLine('  - Rules file (.rules/nexus-agents.md)');\n    writeLine('  - (Skipping MCP/hooks - not needed for standalone mode)');\n  }\n\n  writeEmptyLine();\n  return promptConfirm(rl, 'Proceed with setup?', true);\n}\n\n// ============================================================================\n// Wizard Runner\n// ============================================================================\n\n/**\n * Runs the interactive setup wizard.\n *\n * @returns Setup options based on wizard answers, or undefined if cancelled\n */\nexport async function runWizard(): Promise<Partial<SetupOptions> | undefined> {\n  // Check if interactive mode is available\n  if (!isInteractive()) {\n    writeLine('Interactive mode not available (TTY required).');\n    writeLine('Use --non-interactive flag for automated setup.');\n    return undefined;\n  }\n\n  const rl = createReadline();\n\n  try {\n    printWizardHeader();\n\n    const state: WizardState = {\n      currentStep: 1,\n      totalSteps: 4,\n      answers: {},\n    };\n\n    // Step 1: Usage mode\n    state.answers.usageMode = await askUsageMode(rl, state);\n    state.currentStep++;\n\n    // Step 2: API keys\n    state.answers.hasApiKeys = await askApiKeys(rl, state);\n    state.currentStep++;\n\n    // Step 3: Config directory\n    state.answers.configDirectory = await askConfigDirectory(rl, state);\n    state.currentStep++;\n\n    // Step 4: Confirmation\n    state.answers.confirmProceed = await askConfirmation(rl, state, state.answers);\n    state.currentStep++;\n\n    if (!state.answers.confirmProceed) {\n      writeEmptyLine();\n      writeLine('Setup cancelled.');\n      return undefined;\n    }\n\n    printCompletion();\n\n    // Convert wizard answers to setup options\n    return convertAnswersToOptions(state.answers as WizardAnswers);\n  } finally {\n    rl.close();\n  }\n}\n\n/**\n * Converts wizard answers to setup options.\n */\nfunction convertAnswersToOptions(answers: WizardAnswers): Partial<SetupOptions> {\n  const isStandalone = answers.usageMode === 'standalone';\n\n  return {\n    // Skip MCP and hooks for standalone mode\n    skipMcp: isStandalone,\n    skipHooks: isStandalone,\n    // Always create rules file\n    skipRules: false,\n    // Use user scope for Claude CLI/Desktop, project for standalone\n    scope: isStandalone ? 'project' : 'user',\n    // Non-interactive since we collected all info\n    nonInteractive: true,\n    // Show verbose output to explain what's happening\n    verbose: true,\n  };\n}\n\n// ============================================================================\n// Exports\n// ============================================================================\n\nexport { isInteractive };\n","/**\n * Claude Code permissions snippet generator (#1945).\n *\n * In \"don't ask\" permission mode, Claude Code hard-rejects MCP tool calls\n * that aren't in the allowlist. For nexus-agents to be usable for agentic\n * dogfooding (orchestrate, create_expert, consensus_vote), the tools must\n * be pre-approved in ~/.claude/settings.json.\n *\n * This module generates a recommended snippet for users to paste into\n * their settings.json. We do NOT auto-write permissions — that would be\n * a security footgun.\n *\n * @module cli/setup-permissions\n */\n\n/** MCP tool names that are safe to pre-approve (read-only or idempotent). */\nconst SAFE_READONLY_TOOLS = [\n  'list_experts',\n  'list_workflows',\n  'weather_report',\n  'memory_query',\n  'memory_stats',\n  'query_trace',\n  'research_query',\n  'research_analyze',\n  'research_discover',\n  'research_synthesize',\n  'repo_analyze',\n  'repo_security_plan',\n  'extract_symbols',\n  'search_codebase',\n] as const;\n\n/** MCP tools that execute tasks but are commonly used for dogfooding. */\nconst SAFE_EXECUTION_TOOLS = [\n  'orchestrate',\n  'create_expert',\n  'execute_expert',\n  'consensus_vote',\n  'delegate_to_model',\n  'run_workflow',\n  'issue_triage',\n  'registry_import',\n] as const;\n\nexport type PermissionLevel = 'readonly' | 'all';\n\n/**\n * Generate a JSON snippet of recommended permissions for Claude Code's\n * `~/.claude/settings.json` to pre-approve nexus-agents MCP tools.\n *\n * Users paste this into the `permissions.allow` array.\n */\nexport function generatePermissionsSnippet(level: PermissionLevel = 'all'): string {\n  const tools =\n    level === 'readonly'\n      ? [...SAFE_READONLY_TOOLS]\n      : [...SAFE_READONLY_TOOLS, ...SAFE_EXECUTION_TOOLS];\n\n  const permissions = tools.map((t) => `mcp__nexus-agents__${t}`).sort();\n  return JSON.stringify(permissions, null, 2);\n}\n\n/**\n * Return a human-readable banner explaining the permissions snippet,\n * for inclusion in `nexus-agents setup` output.\n */\nexport function buildPermissionsBanner(snippet: string): string {\n  return [\n    '',\n    '--- Claude Code Permissions (optional) ---',\n    '',\n    \"To use nexus-agents MCP tools in 'don't ask' mode (autonomous/headless\",\n    'Claude Code sessions), add these entries to the `permissions.allow` array',\n    'in your `~/.claude/settings.json`:',\n    '',\n    snippet,\n    '',\n    'Without these, each MCP tool call will prompt for approval in interactive',\n    'mode, or be rejected outright in `dangerously-skip-permissions` mode.',\n    '',\n    'Reference: https://github.com/williamzujkowski/nexus-agents/issues/1945',\n    '',\n  ].join('\\n');\n}\n","/**\n * nexus-agents/cli - Verify Command\n *\n * Quick verification that installation works correctly.\n * No API keys required - runs offline checks only.\n *\n * @module cli/verify-command\n * (Source: Issue #253 - Quick verification step after installation)\n */\n\nimport { VERSION } from '../version.js';\nimport { getTimeProvider } from '../core/index.js';\nimport { defaultConfig } from '../config/index.js';\nimport { BUILT_IN_EXPERTS } from '../agents/experts/expert-config.js';\nimport { colors, symbols } from './ansi-output.js';\nimport { checkSqlite, checkDataDirectory, checkApiKeys } from './doctor.js';\n\n/**\n * Verify command options.\n */\nexport interface VerifyOptions {\n  readonly verbose: boolean;\n}\n\n/**\n * Severity of a failed check.\n *\n * - `hard`: functionality is broken (e.g. Node version too low, core exports\n *   missing). Exit code 1.\n * - `warn`: functionality is degraded but usable (e.g. better-sqlite3 missing\n *   → only some memory backends unavailable; no CLI adapters detected →\n *   orchestrator still works via API keys). Exit code 0.\n *\n * Unused on passing checks.\n */\nexport type VerifySeverity = 'hard' | 'warn';\n\n/**\n * Single verification check result.\n */\nexport interface VerifyCheck {\n  readonly name: string;\n  readonly passed: boolean;\n  readonly message: string;\n  readonly fix?: string;\n  /**\n   * Severity for failed checks. Defaults to `hard` when omitted. Passing\n   * checks ignore this field.\n   */\n  readonly severity?: VerifySeverity;\n}\n\n/**\n * Complete verification result.\n */\nexport interface VerifyResult {\n  readonly version: string;\n  readonly nodeVersion: string;\n  readonly checks: readonly VerifyCheck[];\n  /** True when every check passed. */\n  readonly allPassed: boolean;\n  /**\n   * True when no check failed with `severity: 'hard'`. Drives the exit code:\n   * warnings alone do not fail verification (exit 0 with warnings printed).\n   */\n  readonly noHardFailures: boolean;\n  readonly durationMs: number;\n}\n\n/**\n * Checks if Node.js version is supported.\n */\nfunction checkNodeVersion(): VerifyCheck {\n  const version = process.version;\n  const major = parseInt(version.slice(1).split('.')[0] ?? '0', 10);\n\n  if (major >= 22) {\n    return {\n      name: 'Node.js Version',\n      passed: true,\n      message: `${version} (LTS)`,\n    };\n  }\n\n  if (major >= 18) {\n    return {\n      name: 'Node.js Version',\n      passed: true,\n      message: `${version} (supported, recommend 22.x LTS)`,\n    };\n  }\n\n  return {\n    name: 'Node.js Version',\n    passed: false,\n    message: `${version} (unsupported)`,\n    fix: 'Install Node.js 22.x LTS from https://nodejs.org',\n  };\n}\n\n/**\n * Checks if package exports are accessible.\n */\nfunction checkPackageExports(): VerifyCheck {\n  try {\n    // Check if we can access core exports\n    const hasVersion = typeof VERSION === 'string' && VERSION.length > 0;\n    const hasConfig = typeof defaultConfig === 'object';\n    const hasBuiltInExperts = typeof BUILT_IN_EXPERTS === 'object';\n\n    if (hasVersion && hasConfig && hasBuiltInExperts) {\n      return {\n        name: 'Package Exports',\n        passed: true,\n        message: 'All core modules accessible',\n      };\n    }\n\n    return {\n      name: 'Package Exports',\n      passed: false,\n      message: 'Some modules failed to load',\n      fix: 'Try reinstalling: npm install -g nexus-agents',\n    };\n  } catch {\n    return {\n      name: 'Package Exports',\n      passed: false,\n      message: 'Failed to load core modules',\n      fix: 'Try reinstalling: npm install -g nexus-agents',\n    };\n  }\n}\n\n/**\n * Checks if default configuration is accessible.\n */\nfunction checkConfigLoading(): VerifyCheck {\n  try {\n    const hasModels = typeof defaultConfig.models === 'object';\n    const hasSecurity = typeof defaultConfig.security === 'object';\n\n    if (hasModels && hasSecurity) {\n      return {\n        name: 'Configuration',\n        passed: true,\n        message: 'Default config accessible',\n      };\n    }\n\n    return {\n      name: 'Configuration',\n      passed: true, // Config errors are not fatal for verification\n      message: 'Using default configuration',\n    };\n  } catch {\n    return {\n      name: 'Configuration',\n      passed: true, // Still works with defaults\n      message: 'Using default configuration',\n    };\n  }\n}\n\n/**\n * Checks expert system availability.\n */\nfunction checkExpertSystem(): VerifyCheck {\n  const expertTypes = Object.keys(BUILT_IN_EXPERTS);\n  const count = expertTypes.length;\n\n  if (count >= 5) {\n    return {\n      name: 'Expert System',\n      passed: true,\n      message: `${String(count)} expert types available`,\n    };\n  }\n\n  return {\n    name: 'Expert System',\n    passed: false,\n    message: 'Expert types not loaded',\n    fix: 'Try reinstalling: npm install -g nexus-agents',\n  };\n}\n\n/**\n * Checks that better-sqlite3 loads. Memory backends (agentic, adaptive, typed,\n * mobimem, decay) are unavailable if it's missing — functional degradation,\n * not a hard failure. Rebuilding the native module or reinstalling usually\n * fixes it.\n */\nasync function checkSqliteAvailability(): Promise<VerifyCheck> {\n  const result = await checkSqlite();\n  if (result.available) {\n    return {\n      name: 'SQLite Storage',\n      passed: true,\n      message: 'better-sqlite3 loaded (memory backends available)',\n    };\n  }\n  return {\n    name: 'SQLite Storage',\n    passed: false,\n    severity: 'warn',\n    message: result.error ?? 'better-sqlite3 not available',\n    fix: 'Run \"pnpm rebuild better-sqlite3\" or reinstall nexus-agents',\n  };\n}\n\n/**\n * Checks that the `~/.nexus-agents/` data directories exist and are writable.\n * `cli-commands.ts::dispatchCommand` initializes them lazily (#1398), so\n * missing dirs are a hard failure (persistence will silently drop writes).\n */\nfunction checkDataDirs(): VerifyCheck {\n  const result = checkDataDirectory();\n  const unwritable = result.subdirectories.filter((s) => !s.exists || !s.writable);\n  if (result.rootExists && unwritable.length === 0) {\n    return {\n      name: 'Data Directories',\n      passed: true,\n      message: `${result.rootPath} (all subdirectories writable)`,\n    };\n  }\n  if (!result.rootExists) {\n    return {\n      name: 'Data Directories',\n      passed: false,\n      severity: 'warn',\n      message: `${result.rootPath} does not exist`,\n      fix: 'Run any nexus-agents command — directories auto-initialize on first run',\n    };\n  }\n  return {\n    name: 'Data Directories',\n    passed: false,\n    severity: 'warn',\n    message: `${String(unwritable.length)} subdirectory(ies) unwritable: ${unwritable\n      .map((s) => s.name)\n      .join(', ')}`,\n    fix: `Check filesystem permissions on ${result.rootPath}`,\n  };\n}\n\n/**\n * Checks that at least one execution path is configured — either an API key\n * (direct adapter) or a CLI binary pre-authenticated. Without either, the\n * orchestrator has nothing to dispatch to.\n */\nfunction checkAdapterAvailability(): VerifyCheck {\n  const keys = checkApiKeys();\n  const configured = keys.filter((k) => k.configured);\n  if (configured.length > 0) {\n    return {\n      name: 'Adapter Availability',\n      passed: true,\n      message: `${String(configured.length)} API key(s) configured: ${configured\n        .map((k) => k.name)\n        .join(', ')}`,\n    };\n  }\n  return {\n    name: 'Adapter Availability',\n    passed: false,\n    severity: 'warn',\n    message: 'No API keys configured (ANTHROPIC_API_KEY, OPENAI_API_KEY, GOOGLE_AI_API_KEY)',\n    fix: 'Set at least one API key, or install a CLI (claude/gemini/codex/opencode) and run \"nexus-agents doctor\"',\n  };\n}\n\n/**\n * Runs all verification checks.\n */\nexport async function runVerify(): Promise<VerifyResult> {\n  const time = getTimeProvider();\n  const startTime = time.now();\n\n  const checks: VerifyCheck[] = [\n    checkNodeVersion(),\n    checkPackageExports(),\n    checkConfigLoading(),\n    checkExpertSystem(),\n    await checkSqliteAvailability(),\n    checkDataDirs(),\n    checkAdapterAvailability(),\n  ];\n\n  const allPassed = checks.every((c) => c.passed);\n  const noHardFailures = checks.every((c) => c.passed || c.severity === 'warn');\n  const durationMs = time.now() - startTime;\n\n  return {\n    version: VERSION,\n    nodeVersion: process.version,\n    checks,\n    allPassed,\n    noHardFailures,\n    durationMs,\n  };\n}\n\n/**\n * Formats a single check result.\n *\n * Failed-but-warn checks render as yellow warnings (degraded). Failed hard\n * checks render as red crosses.\n */\nfunction formatCheck(check: VerifyCheck): string {\n  let symbol: string;\n  if (check.passed) {\n    symbol = `${colors.green}${symbols.check}${colors.reset}`;\n  } else if (check.severity === 'warn') {\n    symbol = `${colors.yellow}${symbols.warn}${colors.reset}`;\n  } else {\n    symbol = `${colors.red}${symbols.cross}${colors.reset}`;\n  }\n\n  let line = `  ${symbol} ${check.name}: ${check.message}`;\n\n  if (!check.passed && check.fix !== undefined) {\n    line += `\\n     ${colors.dim}Fix: ${check.fix}${colors.reset}`;\n  }\n\n  return line;\n}\n\n/**\n * Prints verification results to stdout.\n */\nexport function printVerifyResult(result: VerifyResult, verbose: boolean): void {\n  process.stdout.write('\\n');\n  process.stdout.write(`${colors.bold}nexus-agents verify${colors.reset}\\n`);\n  process.stdout.write('===================\\n');\n  process.stdout.write('\\n');\n  process.stdout.write(`Version: ${result.version}\\n`);\n  process.stdout.write(`Node.js: ${result.nodeVersion}\\n`);\n  process.stdout.write('\\n');\n\n  process.stdout.write(`${colors.cyan}Running checks...${colors.reset}\\n`);\n  process.stdout.write('\\n');\n\n  for (const check of result.checks) {\n    process.stdout.write(formatCheck(check) + '\\n');\n  }\n\n  process.stdout.write('\\n');\n\n  const warnCount = result.checks.filter((c) => !c.passed && c.severity === 'warn').length;\n  const hardCount = result.checks.filter((c) => !c.passed && c.severity !== 'warn').length;\n\n  if (result.allPassed) {\n    process.stdout.write(\n      `${colors.green}${colors.bold}Installation verified successfully!${colors.reset}\\n`\n    );\n    process.stdout.write('\\n');\n    process.stdout.write(`${colors.cyan}Next steps:${colors.reset}\\n`);\n    process.stdout.write('  1. Run \"nexus-agents doctor\" to check external CLI integrations\\n');\n    process.stdout.write(\n      '  2. Run \"nexus-agents review --setup\" to configure GitHub integration\\n'\n    );\n    process.stdout.write('  3. Try \"nexus-agents --help\" for all available commands\\n');\n  } else if (hardCount === 0) {\n    process.stdout.write(\n      `${colors.yellow}${colors.bold}Verified with ${String(warnCount)} warning(s) — functional but degraded${colors.reset}\\n`\n    );\n    process.stdout.write('\\n');\n    process.stdout.write('The warnings above indicate reduced functionality but will not\\n');\n    process.stdout.write('prevent nexus-agents from running. Fix them when convenient.\\n');\n  } else {\n    process.stdout.write(\n      `${colors.red}${colors.bold}Verification failed: ${String(hardCount)} blocking issue(s), ${String(warnCount)} warning(s)${colors.reset}\\n`\n    );\n    process.stdout.write('\\n');\n    process.stdout.write('Please fix the blocking issues above and try again.\\n');\n  }\n\n  process.stdout.write('\\n');\n\n  if (verbose) {\n    process.stdout.write(`${colors.dim}Duration: ${String(result.durationMs)}ms${colors.reset}\\n`);\n    process.stdout.write('\\n');\n  }\n}\n\n/**\n * Runs the verify command and prints results.\n *\n * Exit codes:\n * - `0`: all checks passed, or only `warn`-severity checks failed (degraded\n *   but functional)\n * - `1`: at least one `hard`-severity check failed (broken install)\n */\nexport async function verifyCommand(options: VerifyOptions): Promise<number> {\n  const result = await runVerify();\n  printVerifyResult(result, options.verbose);\n  return result.noHardFailures ? 0 : 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package/dist/chunk-NUBSJGQZ.js

@@ -0,0 +1,14 @@
+// src/security/safe-path.ts
+import { resolve, sep } from "path";
+function resolveInsideRoot(filePath, root = process.cwd()) {
+  const resolvedRoot = resolve(root);
+  const resolved = resolve(resolvedRoot, filePath);
+  if (resolved === resolvedRoot) return resolved;
+  if (resolved.startsWith(resolvedRoot + sep)) return resolved;
+  return null;
+}
+
+export {
+  resolveInsideRoot
+};
+//# sourceMappingURL=chunk-NUBSJGQZ.js.map

package/dist/chunk-NUBSJGQZ.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/security/safe-path.ts"],"sourcesContent":["/**\n * Safe Path — Path traversal guards for scanner-controlled inputs (#1813, #1814)\n *\n * When reading files whose path comes from untrusted input (e.g., SARIF\n * scanner output), we must verify the resolved path stays within the\n * workspace root. Without this, a malicious scanner can cause arbitrary\n * file reads whose contents are exfiltrated via downstream LLM prompts\n * (CWE-22).\n *\n * Shared helper to prevent the finding-triage/fix-generator drift that\n * required two separate fixes.\n *\n * @module security/safe-path\n */\n\nimport { resolve, sep } from 'node:path';\n\n/**\n * Resolve a scanner-supplied path against the workspace root, returning null\n * if it escapes. Null means the caller must fall back to a safe alternative\n * (e.g., scanner-provided snippet) rather than reading the file.\n *\n * @param filePath - Scanner-supplied path (may be relative or absolute)\n * @param root - Workspace root (defaults to process.cwd())\n * @returns Resolved absolute path if inside root, null otherwise\n */\nexport function resolveInsideRoot(filePath: string, root: string = process.cwd()): string | null {\n  const resolvedRoot = resolve(root);\n  const resolved = resolve(resolvedRoot, filePath);\n  if (resolved === resolvedRoot) return resolved;\n  if (resolved.startsWith(resolvedRoot + sep)) return resolved;\n  return null;\n}\n"],"mappings":";AAeA,SAAS,SAAS,WAAW;AAWtB,SAAS,kBAAkB,UAAkB,OAAe,QAAQ,IAAI,GAAkB;AAC/F,QAAM,eAAe,QAAQ,IAAI;AACjC,QAAM,WAAW,QAAQ,cAAc,QAAQ;AAC/C,MAAI,aAAa,aAAc,QAAO;AACtC,MAAI,SAAS,WAAW,eAAe,GAAG,EAAG,QAAO;AACpD,SAAO;AACT;","names":[]}

package/dist/{chunk-JERFBN73.js → chunk-PCMWLXT4.js}

@@ -1,3 +1,6 @@
+import {
+  resolveInsideRoot
+} from "./chunk-NUBSJGQZ.js";
 import {
   ParseError,
   SecurityError,
@@ -6,19 +9,7 @@ import {
 
 // src/cli/research-helpers-io.ts
 import * as fs from "fs/promises";
-import { join, resolve as resolve2 } from "path";
-
-// src/security/safe-path.ts
-import { resolve, sep } from "path";
-function resolveInsideRoot(filePath, root = process.cwd()) {
-  const resolvedRoot = resolve(root);
-  const resolved = resolve(resolvedRoot, filePath);
-  if (resolved === resolvedRoot) return resolved;
-  if (resolved.startsWith(resolvedRoot + sep)) return resolved;
-  return null;
-}
-
-// src/cli/research-helpers-io.ts
+import { join, resolve } from "path";
 import { parse as parseYaml, stringify as stringifyYaml } from "yaml";
 var REGISTRY_PATH = "docs/research/registry";
 var TECHNIQUES_FILE = "techniques.yaml";
@@ -32,7 +23,7 @@ function validatePath(constructedPath, allowedRoot) {
     return {
       ok: false,
       error: new SecurityError("Path traversal detected: path escapes allowed root directory", {
-        context: { constructedPath, allowedRoot: resolve2(allowedRoot) }
+        context: { constructedPath, allowedRoot: resolve(allowedRoot) }
       })
     };
   }
@@ -919,7 +910,6 @@ function deduplicateFindings(findings) {
 }
 
 export {
-  resolveInsideRoot,
   REGISTRY_PATH,
   getProjectRoot,
   loadTechniquesRegistry,
@@ -928,4 +918,4 @@ export {
   normalizeTopicToCanonical,
   synthesizeResearch
 };
-//# sourceMappingURL=chunk-JERFBN73.js.map
+//# sourceMappingURL=chunk-PCMWLXT4.js.map

package/dist/chunk-PCMWLXT4.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/research-helpers-io.ts","../src/cli/research-alignment-map.ts","../src/research/topic-aliases.ts","../src/cli/research-helpers-synthesize.ts"],"sourcesContent":["/**\n * Research Registry I/O Operations\n *\n * File operations for loading and saving research registry YAML files.\n * Includes path traversal protection per Issue #353.\n *\n * @see docs/research/RESEARCH_INDEX.md\n * @see Issue #237 (Epic #225)\n * @see Issue #353 (Security - Path traversal fix)\n */\n\nimport * as fs from 'node:fs/promises';\nimport { join, resolve } from 'node:path';\nimport { resolveInsideRoot } from '../security/safe-path.js';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport type { Result } from '../core/index.js';\nimport { SecurityError, getErrorMessage } from '../core/index.js';\nimport { ParseError } from '../core/types/workflow.js';\nimport type { TechniquesRegistry, PapersRegistry } from './research-types.js';\n\n// =============================================================================\n// CONSTANTS\n// =============================================================================\n\n/** Path to research registry directory relative to project root */\nexport const REGISTRY_PATH = 'docs/research/registry';\n\n/** Filename for techniques registry */\nexport const TECHNIQUES_FILE = 'techniques.yaml';\n\n/** Filename for papers registry */\nexport const PAPERS_FILE = 'papers.yaml';\n\n// =============================================================================\n// PROJECT ROOT\n// =============================================================================\n\n/**\n * Get the project root directory.\n * Note: Returns cwd since registry operations use explicit rootDir parameter\n */\nexport function getProjectRoot(): string {\n  return process.cwd();\n}\n\n// =============================================================================\n// PATH VALIDATION\n// =============================================================================\n\n/**\n * Validates that a constructed path stays within the allowed root directory.\n * Prevents path traversal attacks (e.g., ../../../etc/passwd).\n *\n * @param constructedPath - The full path to validate\n * @param allowedRoot - The root directory that paths must be within\n * @returns Result with validated absolute path or SecurityError\n */\nfunction validatePath(constructedPath: string, allowedRoot: string): Result<string, SecurityError> {\n  const resolved = resolveInsideRoot(constructedPath, allowedRoot);\n  if (resolved === null) {\n    return {\n      ok: false,\n      error: new SecurityError('Path traversal detected: path escapes allowed root directory', {\n        context: { constructedPath, allowedRoot: resolve(allowedRoot) },\n      }),\n    };\n  }\n  return { ok: true, value: resolved };\n}\n\n// =============================================================================\n// LOAD OPERATIONS\n// =============================================================================\n\n/**\n * Load techniques registry from YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with TechniquesRegistry or SecurityError/ParseError\n */\nexport async function loadTechniquesRegistry(\n  rootDir?: string\n): Promise<Result<TechniquesRegistry, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, TECHNIQUES_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  try {\n    const content = await fs.readFile(pathValidation.value, 'utf-8');\n    return { ok: true, value: parseYaml(content) as TechniquesRegistry };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to load techniques registry: ${message}`) };\n  }\n}\n\n/**\n * Load papers registry from YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with PapersRegistry or SecurityError/ParseError\n */\nexport async function loadPapersRegistry(\n  rootDir?: string\n): Promise<Result<PapersRegistry, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  try {\n    const content = await fs.readFile(pathValidation.value, 'utf-8');\n    return { ok: true, value: parseYaml(content) as PapersRegistry };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to load papers registry: ${message}`) };\n  }\n}\n\n// =============================================================================\n// SAVE OPERATIONS\n// =============================================================================\n\n/**\n * Save techniques registry to YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param registry - The techniques registry to save\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with void on success or SecurityError/ParseError on failure\n */\nexport async function saveTechniquesRegistry(\n  registry: TechniquesRegistry,\n  rootDir?: string\n): Promise<Result<void, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, TECHNIQUES_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  try {\n    const content = stringifyYaml(registry, { lineWidth: 100 });\n    await fs.writeFile(pathValidation.value, content, 'utf-8');\n    return { ok: true, value: undefined };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to save techniques registry: ${message}`) };\n  }\n}\n\n/**\n * Save papers registry to YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param registry - The papers registry to save\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with void on success or SecurityError/ParseError on failure\n */\nexport async function savePapersRegistry(\n  registry: PapersRegistry,\n  rootDir?: string\n): Promise<Result<void, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  try {\n    const content = stringifyYaml(registry, { lineWidth: 100 });\n    await fs.writeFile(pathValidation.value, content, 'utf-8');\n    return { ok: true, value: undefined };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to save papers registry: ${message}`) };\n  }\n}\n","/**\n * Research Alignment Map\n *\n * Maps technique names from the research registry to canonical code paths\n * in the nexus-agents codebase. Used by research synthesis to determine\n * which paper techniques are implemented, partially implemented, or new.\n *\n * @module cli/research-alignment-map\n * (Source: Issue #1386 — Research Synthesis Pipeline)\n */\n\n// =============================================================================\n// TYPES\n// =============================================================================\n\n/** Implementation status for a mapped technique. */\nexport interface TechniqueMapping {\n  readonly status: 'implemented' | 'partial';\n  readonly path: string;\n  readonly hint?: string | undefined;\n}\n\n/** A feature gate that controls an implementation. */\nexport interface FeatureGate {\n  /** Environment variable or config key. */\n  readonly envVar: string;\n  /** Default value when not explicitly set. */\n  readonly defaultValue: string;\n  /** Brief description of what the gate controls. */\n  readonly description: string;\n  /** Related technique names from the alignment map (if any). */\n  readonly techniques?: readonly string[];\n}\n\n// =============================================================================\n// MAP\n// =============================================================================\n\n/**\n * Maps technique names to canonical code paths.\n * 'implemented' = full implementation exists matching the technique.\n * 'partial' = related code exists but doesn't fully implement the technique.\n */\nexport const TECHNIQUE_IMPLEMENTATION_MAP: ReadonlyMap<string, TechniqueMapping> = new Map([\n  // Routing techniques\n  ['linucb-routing', { status: 'implemented', path: 'cli-adapters/linucb-bandit.ts' }],\n  ['topsis-routing', { status: 'implemented', path: 'cli-adapters/topsis-router.ts' }],\n  [\n    'cascade-routing',\n    { status: 'implemented', path: 'routing/stages/confidence-cascade-stage.ts' },\n  ],\n  [\n    'complexity-based-routing',\n    { status: 'implemented', path: 'routing/stages/confidence-cascade-stage.ts' },\n  ],\n  [\n    'moe-routing',\n    {\n      status: 'implemented',\n      path: 'cli-adapters/composite-router.ts',\n      hint: '5-stage composite routing selects among specialized CLI experts based on task features',\n    },\n  ],\n  ['two-stage-routing', { status: 'implemented', path: 'cli-adapters/composite-router-stages.ts' }],\n  [\n    'capability-instruction-tuning',\n    {\n      status: 'partial',\n      path: 'routing/stages/capability-match-stage.ts',\n      hint: 'Static capability profiles, not instruction-tuned',\n    },\n  ],\n  [\n    'knn-routing',\n    {\n      status: 'implemented',\n      path: 'routing/stages/knn-routing-stage.ts',\n      hint: 'KnnRoutingStage: cosine similarity over keyword vectors, K-nearest experience patterns, weighted by success rate',\n    },\n  ],\n  ['pilot-budget-routing', { status: 'implemented', path: 'cli-adapters/budget-router.ts' }],\n  [\n    'tolerance-routing',\n    {\n      status: 'implemented',\n      path: 'cli-adapters/composite-router-helpers.ts',\n      hint: 'TOPSIS_TOLERANCE_BAND_PERCENT (5%) identifies quality-equivalent candidates after TOPSIS ranking',\n    },\n  ],\n  [\n    'sater-routing',\n    {\n      status: 'implemented',\n      path: 'routing/stages/quality-constraint-stage.ts',\n      hint: 'QualityConstraintStage filters models by min quality (0.7), max cost, max latency before selection',\n    },\n  ],\n  [\n    'preference-trained-routing',\n    { status: 'implemented', path: 'cli-adapters/preference-router.ts' },\n  ],\n  [\n    'strmac-state-routing',\n    {\n      status: 'implemented',\n      path: 'context/routing-memory.ts',\n      hint: 'RoutingMemory maintains state across calls (profile, experience, action cache) feeding LinUCB + weather bonus stages',\n    },\n  ],\n  [\n    'cross-attention-routing',\n    {\n      status: 'implemented',\n      path: 'routing/stages/capability-match-stage.ts',\n      hint: 'AttentionMatrix maps task features to capability weights (configurable cross-attention)',\n    },\n  ],\n\n  // Consensus techniques\n  ['consensus-protocol', { status: 'implemented', path: 'consensus/engine.ts' }],\n  ['majority-voting', { status: 'implemented', path: 'consensus/engine.ts' }],\n  ['higher-order-voting', { status: 'implemented', path: 'consensus/higher-order-strategy.ts' }],\n  [\n    'anti-conformity-weighting',\n    { status: 'implemented', path: 'consensus/higher-order-strategy.ts' },\n  ],\n  [\n    'agreement-based-cascading',\n    {\n      status: 'implemented',\n      path: 'consensus/engine.ts',\n      hint: 'canCascadeEarly() closes proposals when outcome is mathematically determined',\n    },\n  ],\n  [\n    'incremental-quorum',\n    {\n      status: 'implemented',\n      path: 'consensus/incremental-quorum.ts',\n      hint: 'Ambiguity detection + voter expansion via VoterExpansionCallback (#1408)',\n    },\n  ],\n  [\n    'aegean-consensus',\n    { status: 'partial', path: 'consensus/engine.ts', hint: 'Byzantine tolerance not implemented' },\n  ],\n  [\n    'cp-wbft-consensus',\n    {\n      status: 'partial',\n      path: 'consensus/engine.ts',\n      hint: 'No weighted Byzantine fault tolerance',\n    },\n  ],\n\n  // Memory techniques\n  ['adaptive-memory', { status: 'implemented', path: 'memory/adaptive/' }],\n  ['mirix-six-type-memory', { status: 'implemented', path: 'memory/typed/' }],\n  [\n    'mem0-memory-architecture',\n    { status: 'partial', path: 'memory/', hint: 'Multi-backend memory but not mem0 pattern' },\n  ],\n  [\n    'graph-based-memory',\n    {\n      status: 'partial',\n      path: 'memory/belief/',\n      hint: 'Belief triples are graph-like but not full graph DB',\n    },\n  ],\n  ['experience-memory', { status: 'implemented', path: 'memory/session/' }],\n  ['hindsight-belief-memory', { status: 'implemented', path: 'memory/belief/' }],\n  [\n    'profile-memory',\n    {\n      status: 'implemented',\n      path: 'context/routing-memory.ts',\n      hint: 'RoutingMemory stores model preferences per task type and feeds recommendations into composite router via PERSISTENCE_AWARE_FLAGS',\n    },\n  ],\n  [\n    'action-memory',\n    {\n      status: 'implemented',\n      path: 'orchestration/outcomes/',\n      hint: 'OutcomeStore records actions+results+context with query-by-category/CLI/time and cross-session persistence',\n    },\n  ],\n  ['reflection-memory', { status: 'implemented', path: 'mcp/tools/orchestrate-reflection.ts' }],\n  [\n    'history-encoding',\n    {\n      status: 'partial',\n      path: 'context/token-counter.ts',\n      hint: 'Token counting exists but no learned history encoding',\n    },\n  ],\n\n  // Orchestration techniques\n  [\n    'aflow-mcts-workflows',\n    {\n      status: 'partial',\n      path: 'workflows/aflow/',\n      hint: 'AFlow scaffolding exists but MCTS not implemented',\n    },\n  ],\n  [\n    'dynamic-agent-selection',\n    { status: 'implemented', path: 'orchestration/aorchestra/agent-planner.ts' },\n  ],\n  ['dynamic-subagent-creation', { status: 'implemented', path: 'mcp/tools/create-expert.ts' }],\n  ['role-based-protocols', { status: 'implemented', path: 'agents/expert-roles.ts' }],\n  [\n    'rule-based-coordination',\n    { status: 'implemented', path: 'orchestration/aorchestra/worker-dispatcher.ts' },\n  ],\n  [\n    'temporal-graph-orchestration',\n    {\n      status: 'partial',\n      path: 'orchestration/graph/',\n      hint: 'Graph workflows exist but not temporal-aware',\n    },\n  ],\n  [\n    'model-based-coordination',\n    {\n      status: 'partial',\n      path: 'orchestration/aorchestra/',\n      hint: 'Worker dispatch but not model-based coordination theory',\n    },\n  ],\n  [\n    'trinity-roles',\n    {\n      status: 'partial',\n      path: 'agents/expert-roles.ts',\n      hint: '10 expert roles, not trinity pattern',\n    },\n  ],\n  [\n    'sew-self-evolving-workflows',\n    {\n      status: 'partial',\n      path: 'workflows/aflow/',\n      hint: 'AFlow framework but no self-evolution loop',\n    },\n  ],\n  [\n    'scaling-coordination-predictor',\n    {\n      status: 'partial',\n      path: 'orchestration/aorchestra/agent-planner.ts',\n      hint: 'Wave sizing but no scaling prediction',\n    },\n  ],\n\n  // Learning techniques\n  [\n    'self-refine-loop',\n    {\n      status: 'implemented',\n      path: 'mcp/tools/orchestrate-dispatch.ts',\n    },\n  ],\n  [\n    'recursive-improvement',\n    {\n      status: 'implemented',\n      path: 'mcp/tools/orchestrate-dispatch.ts',\n    },\n  ],\n  [\n    'rl-orchestrator',\n    {\n      status: 'implemented',\n      path: 'cli-adapters/linucb-bandit.ts',\n      hint: 'LinUCB contextual bandit actively selects models via explore-exploit in routing pipeline',\n    },\n  ],\n  ['reflexion-verbal-rl', { status: 'implemented', path: 'mcp/tools/orchestrate-reflection.ts' }],\n\n  // Source-derived techniques (Wave 6 — from open-source project analysis)\n  ['failure-lesson-injection', { status: 'implemented', path: 'orchestration/failure-lessons.ts' }],\n  [\n    'skill-relevance-matching',\n    {\n      status: 'implemented',\n      path: 'agents/experts/skill-matcher.ts',\n      hint: 'Matches task keywords to agent skill descriptions for optimal routing',\n    },\n  ],\n  [\n    'context-rot-prevention',\n    {\n      status: 'implemented',\n      path: 'agents/context-pruner.ts',\n      hint: 'Token-efficient context pruning prevents quality degradation in long sessions',\n    },\n  ],\n  [\n    'wave-based-parallel-execution',\n    {\n      status: 'implemented',\n      path: 'orchestration/aorchestra/worker-dispatcher.ts',\n      hint: 'AOrchestra worker dispatch with cross-wave context sharing',\n    },\n  ],\n  [\n    'write-time-deduplication',\n    {\n      status: 'implemented',\n      path: 'mcp/tools/memory-write.ts',\n      hint: 'Semantic dedup at write time prevents memory bloat',\n    },\n  ],\n]);\n\n// =============================================================================\n// FEATURE GATE INVENTORY\n// =============================================================================\n\n/** Inventory of feature gates linked to research-aligned techniques. */\nexport const FEATURE_GATE_INVENTORY: readonly FeatureGate[] = [\n  {\n    envVar: 'NEXUS_V2_MODE',\n    defaultValue: 'full',\n    description: 'V2 pipeline mode (off/partial/full)',\n    techniques: ['two-stage-routing', 'cascade-routing'],\n  },\n  {\n    envVar: 'NEXUS_AORCHESTRA',\n    defaultValue: 'true',\n    description: 'AOrchestra dynamic agent planning',\n    techniques: ['dynamic-agent-selection', 'model-based-coordination'],\n  },\n  {\n    envVar: 'NEXUS_AORCHESTRA_DISPATCH',\n    defaultValue: 'true',\n    description: 'AOrchestra worker dispatch',\n    techniques: ['rule-based-coordination', 'self-refine-loop'],\n  },\n  {\n    envVar: 'NEXUS_PERSIST_LEARNING',\n    defaultValue: 'true',\n    description: 'Cross-session routing persistence',\n    techniques: ['linucb-routing', 'preference-trained-routing', 'experience-memory'],\n  },\n  {\n    envVar: 'NEXUS_REFLECTIVE_MEMORY',\n    defaultValue: 'shadow',\n    description: 'Reflective memory retrieval (shadow=default, true=full, false=off)',\n    techniques: ['reflection-memory', 'adaptive-memory', 'reflexion-verbal-rl'],\n  },\n  {\n    envVar: 'NEXUS_BILLING_MODE',\n    defaultValue: 'plan',\n    description: 'Cost mode (plan=strongest, api=cost-aware)',\n    techniques: ['pilot-budget-routing', 'topsis-routing'],\n  },\n  {\n    envVar: 'NEXUS_WORKER_MAX_CALLS',\n    defaultValue: '6',\n    description: 'Max model calls per orchestrate',\n    techniques: ['self-refine-loop', 'recursive-improvement'],\n  },\n  { envVar: 'NEXUS_AUTH_ENABLED', defaultValue: 'true', description: 'Server authentication' },\n  { envVar: 'NEXUS_EVENTBUS_ENABLED', defaultValue: 'true', description: 'EventBus A2A bridge' },\n  {\n    envVar: 'NEXUS_RATE_LIMIT_ENABLED',\n    defaultValue: 'true',\n    description: 'Token-bucket rate limiter',\n  },\n  {\n    envVar: 'NEXUS_CIRCUIT_BREAKER_THRESHOLD',\n    defaultValue: '5',\n    description: 'Circuit breaker failure threshold',\n  },\n  {\n    envVar: 'NEXUS_V2_POLICY_MODE',\n    defaultValue: 'block',\n    description: 'Policy enforcement (off/warn/block)',\n  },\n  { envVar: 'NEXUS_LOG_LEVEL', defaultValue: 'info', description: 'Logging verbosity' },\n  {\n    envVar: 'NEXUS_DISABLE_SESSIONS',\n    defaultValue: 'false',\n    description: 'Disable session tracking',\n  },\n  {\n    envVar: 'NEXUS_DISABLE_METRICS',\n    defaultValue: 'false',\n    description: 'Disable metrics tracking',\n  },\n  {\n    envVar: 'NEXUS_ALLOW_MOCK_ORCHESTRATION',\n    defaultValue: 'false',\n    description: 'Allow mock orchestration (test/CI)',\n  },\n  {\n    envVar: 'NEXUS_MAX_CONCURRENT_EXPERTS',\n    defaultValue: '6',\n    description: 'Expert pool semaphore capacity',\n  },\n  {\n    envVar: 'NEXUS_VOTE_TIMEOUT_MS',\n    defaultValue: '60000',\n    description: 'Consensus vote timeout override',\n  },\n  {\n    envVar: 'NEXUS_EXPERT_TIMEOUT_MS',\n    defaultValue: '120000',\n    description: 'Expert handler timeout override',\n  },\n  {\n    envVar: 'NEXUS_WORKER_TIMEOUT_MS',\n    defaultValue: '60000',\n    description: 'Worker subprocess timeout override',\n  },\n];\n","/**\n * Topic alias map for normalizing free-form topic strings to canonical topics.\n *\n * Maps 200+ free-form topic strings found in papers.yaml to 12 canonical topics.\n * Used by normalizeTopicToCanonical() in research-schemas.ts.\n *\n * @module research/topic-aliases\n * @see Issue #1578 — Topic taxonomy normalization\n */\n\n/**\n * Map of free-form topic strings to canonical topics.\n */\nexport const TOPIC_ALIASES: Readonly<Record<string, string>> = {\n  // → consensus\n  voting: 'consensus',\n  'consensus-voting': 'consensus',\n  debate: 'consensus',\n  quorum: 'consensus',\n  byzantine: 'consensus',\n  'anti-conformity': 'consensus',\n  'agreement-based': 'consensus',\n  'correlation-aware': 'consensus',\n  'LLM consensus and multi-agent voting mechanisms': 'consensus',\n  'tolerance-parameter': 'consensus',\n\n  // → routing\n  'model-routing': 'routing',\n  'model routing': 'routing',\n  'llm-routing': 'routing',\n  cascade: 'routing',\n  'cascade-routing': 'routing',\n  'cost-optimization': 'routing',\n  'cost-reduction': 'routing',\n  'model-selection': 'routing',\n  topsis: 'routing',\n  linucb: 'routing',\n  'contextual-bandit': 'routing',\n  'quality-constrained': 'routing',\n  'budget-constraints': 'routing',\n  'unified-routing': 'routing',\n  'query-model-matching': 'routing',\n  'adaptive model routing and selection optimization': 'routing',\n  'multi-model routing optimization': 'routing',\n  'Single-head cross-attention for query-model matching': 'routing',\n  'performance-cost-tradeoff': 'routing',\n  'task-routing': 'routing',\n  'difficulty-estimation': 'routing',\n  'score-based': 'routing',\n  'optimal-weighting': 'routing',\n  'hierarchical-filtering': 'routing',\n  'preference-optimization': 'routing',\n  'preference-data': 'routing',\n  dpo: 'routing',\n  'cross-attention': 'routing',\n  'cma-es': 'routing',\n  profile: 'routing',\n  prediction: 'routing',\n  lightweight: 'routing',\n  bayesian: 'routing',\n  'quality-diversity': 'routing',\n  'resource-optimization': 'routing',\n  'routing-latency': 'routing',\n  optimization: 'routing',\n  'model-merging': 'routing',\n  'model-zoo': 'routing',\n\n  // → memory\n  'context-management': 'memory',\n  'context-compression': 'memory',\n  'context-control': 'memory',\n  compression: 'memory',\n  'kv-cache': 'memory',\n  'long-context': 'memory',\n  'long-term-memory': 'memory',\n  'episodic-memory': 'memory',\n  'graph-memory': 'memory',\n  'hierarchical-memory': 'memory',\n  'agentic-memory': 'memory',\n  'lifelong-learning': 'memory',\n  'cross-session-learning': 'memory',\n  'continual-learning': 'memory',\n  'self-editing-memory': 'memory',\n  'six-type-memory': 'memory',\n  'belief-memory': 'memory',\n  'belief-state': 'memory',\n  'action-memory': 'memory',\n  'memory-evolution': 'memory',\n  'virtual-context': 'memory',\n  paging: 'memory',\n  'prompt-compression': 'memory',\n  'learned-compression': 'memory',\n  zettelkasten: 'memory',\n  'knowledge-distillation': 'memory',\n  'history-encoding': 'memory',\n  'ictm-tuple': 'memory',\n  'latent-space': 'memory',\n  'vector-db': 'memory',\n  embedding: 'memory',\n  'Taxonomy of context management strategies': 'memory',\n  'Task-specific context compression': 'memory',\n  'Learned compression modules': 'memory',\n  rag: 'memory',\n  'retrieval augmented generation': 'memory',\n  svd: 'memory',\n  'svd-mutation': 'memory',\n  vae: 'memory',\n  knn: 'memory',\n  experience: 'memory',\n  'state-aware': 'memory',\n  'temporal-graph': 'memory',\n  versioning: 'memory',\n\n  // → code-generation\n  'code-repair': 'code-generation',\n  'code-agent': 'code-generation',\n  'code-review': 'code-generation',\n  'software-engineering': 'code-generation',\n  'swe-bench': 'code-generation',\n  'self-improvement': 'code-generation',\n  'self-evolving': 'code-generation',\n  'self-debug': 'code-generation',\n  'self-modification': 'code-generation',\n  'skill-library': 'code-generation',\n  'skill-discovery': 'code-generation',\n  'code review benchmarks': 'code-generation',\n  'code generation evaluation': 'code-generation',\n  'execution-feedback': 'code-generation',\n\n  // → cli-tools\n  mcp: 'cli-tools',\n  'MCP protocol': 'cli-tools',\n  'MCP security': 'cli-tools',\n  'MCP Security': 'cli-tools',\n  'mcp-applications': 'cli-tools',\n  'model-context-protocol': 'cli-tools',\n  puppeteer: 'cli-tools',\n  streaming: 'cli-tools',\n  integration: 'cli-tools',\n\n  // → orchestration\n  'multi-agent': 'orchestration',\n  'multi-agent-systems': 'orchestration',\n  'multi-agent orchestration': 'orchestration',\n  'Multi-Agent Orchestration': 'orchestration',\n  'multi-agent-orchestration': 'orchestration',\n  'multi-agent coordination': 'orchestration',\n  'multi-agent-coordination': 'orchestration',\n  'multi-agent-worker-dispatch': 'orchestration',\n  'multi-agent reliability': 'orchestration',\n  'multi-agent-rl': 'orchestration',\n  coordination: 'orchestration',\n  coordinator: 'orchestration',\n  collaboration: 'orchestration',\n  'graph-orchestration': 'orchestration',\n  'agent architecture': 'orchestration',\n  'dynamic-agent-creation': 'orchestration',\n  'specialized-agents': 'orchestration',\n  'thinker-worker-verifier': 'orchestration',\n  'two-agent': 'orchestration',\n  'meta-agent': 'orchestration',\n  agents: 'orchestration',\n  'workflow-optimization': 'orchestration',\n  'workflow-generation': 'orchestration',\n  'agent-communication': 'orchestration',\n  'inter-agent': 'orchestration',\n  'gvu-operator': 'orchestration',\n  'rubber-duck': 'orchestration',\n  'parallel-exploration': 'orchestration',\n  kubernetes: 'orchestration',\n  'scale-to-zero': 'orchestration',\n  edge: 'orchestration',\n  llm: 'orchestration',\n  multimodal: 'orchestration',\n  production: 'orchestration',\n  hybrid: 'orchestration',\n  'automatic-discovery': 'orchestration',\n  roadmap: 'orchestration',\n\n  // → security\n  'prompt injection defense': 'security',\n  'inter-agent-security': 'security',\n  'agent security': 'security',\n  compliance: 'security',\n  'formal-verification': 'security',\n  'formal-safety': 'security',\n\n  // → evaluation\n  benchmark: 'evaluation',\n  benchmarking: 'evaluation',\n  survey: 'evaluation',\n  'autonomous agent evaluation benchmarks': 'evaluation',\n  'evaluation-methods': 'evaluation',\n  'LLM evaluation': 'evaluation',\n  'hallucination-detection': 'evaluation',\n  'self-evaluation': 'evaluation',\n  'confidence-probe': 'evaluation',\n  'confidence-aware': 'evaluation',\n  verifier: 'evaluation',\n  observability: 'evaluation',\n  theoretical: 'evaluation',\n  'post-deployment': 'evaluation',\n  capability: 'evaluation',\n  'knowledge-gaps': 'evaluation',\n  helm: 'evaluation',\n\n  // → safety\n  'agentic-safety': 'safety',\n  'agentic AI safety': 'safety',\n  'safety-evaluation': 'safety',\n  'reward-modeling': 'safety',\n  'constitutional-ai': 'safety',\n  'hazard-analysis': 'safety',\n  stpa: 'safety',\n  'risk-assessment': 'safety',\n  'fault-tolerance': 'safety',\n  'ai-feedback': 'safety',\n  rlaif: 'safety',\n  'human-in-the-loop': 'safety',\n  feedback: 'safety',\n  'feedback-loop': 'safety',\n  'feedback-learning': 'safety',\n  anthropic: 'safety',\n\n  // → planning\n  'decision-making': 'planning',\n  'tree-search': 'planning',\n  'tree-structure': 'planning',\n  'multi-tree': 'planning',\n  mcts: 'planning',\n  backtrack: 'planning',\n  hindsight: 'planning',\n  'task-specific': 'planning',\n\n  // → tool-use\n  'tool use': 'tool-use',\n  'tool-augmented reasoning and function calling': 'tool-use',\n  'tool routing optimization': 'tool-use',\n  'dynamic-linking': 'tool-use',\n  'Sparse outcome rewards reduce tool calls by 72%': 'tool-use',\n\n  // → reasoning\n  'test-time': 'reasoning',\n  'test-time-scaling': 'reasoning',\n  'inference-scaling': 'reasoning',\n  'inference-optimization': 'reasoning',\n  'self-critique': 'reasoning',\n  'self-reflection': 'reasoning',\n  'self-referential': 'reasoning',\n  'self-play': 'reasoning',\n  reflexion: 'reasoning',\n  reflection: 'reasoning',\n  'reasoning-optimization': 'reasoning',\n  'meta-thinking': 'reasoning',\n  scaling: 'reasoning',\n  recursive: 'reasoning',\n  'trajectory-abstraction': 'reasoning',\n  'verbal-rl': 'reasoning',\n  exploration: 'reasoning',\n  'Reducible uncertainty modeling across agent trajectories': 'reasoning',\n  'Environmental feedback reduces uncertainty at decision gates': 'reasoning',\n  'reinforcement-learning': 'reasoning',\n  transformer: 'reasoning',\n  ssm: 'reasoning',\n  'sparse-activation': 'reasoning',\n  'behavior-distillation': 'reasoning',\n  'training-free': 'reasoning',\n  'transfer-learning': 'reasoning',\n  'instruction-tuning': 'reasoning',\n  'Dense process rewards improve performance by 22%': 'reasoning',\n  'prompt-optimization': 'reasoning',\n};\n\n/**\n * Normalize a free-form topic string to a canonical topic.\n * Returns the canonical topic if a mapping exists, otherwise the original string.\n */\nexport function normalizeTopicToCanonical(topic: string): string {\n  return TOPIC_ALIASES[topic] ?? topic;\n}\n","/**\n * Research Synthesis Helper\n *\n * Groups papers by topic cluster and generates structured synthesis\n * summaries with themes, findings, and implementation opportunities.\n *\n * @module cli/research-helpers-synthesize\n * (Source: Issue #1386 — Research Synthesis Pipeline)\n */\n\nimport { loadPapersRegistry } from './research-helpers-io.js';\nimport type { PapersRegistry } from './research-types.js';\nimport type { Result } from '../core/result.js';\nimport { getErrorMessage } from '../core/index.js';\nimport { TECHNIQUE_IMPLEMENTATION_MAP, FEATURE_GATE_INVENTORY } from './research-alignment-map.js';\nimport { normalizeTopicToCanonical } from '../research/topic-aliases.js';\n\n// =============================================================================\n// TYPES\n// =============================================================================\n\n/** A paper entry from the registry, simplified for synthesis. */\nexport interface SynthesisPaper {\n  readonly id: string;\n  readonly title: string;\n  readonly topics: readonly string[];\n  readonly tags: readonly string[];\n  readonly summary: string;\n  readonly keyFindings: readonly string[];\n  readonly relevance: string;\n  readonly implementationStatus: string;\n  readonly techniquesExtracted: readonly string[];\n  readonly qualityScore: number;\n  readonly evidenceTier: 'high' | 'medium' | 'low';\n}\n\n/** A cluster of related papers grouped by topic. */\nexport interface PaperCluster {\n  readonly topic: string;\n  readonly papers: readonly SynthesisPaper[];\n  readonly paperCount: number;\n}\n\n/** A technique aligned to an existing implementation. */\nexport interface TechniqueAlignment {\n  readonly technique: string;\n  readonly status: 'implemented' | 'partial' | 'not-started';\n  readonly canonicalPath?: string | undefined;\n  readonly improvementHint?: string | undefined;\n}\n\n/** Quality distribution within a cluster. */\nexport interface QualityDistribution {\n  readonly avgScore: number;\n  readonly high: number;\n  readonly medium: number;\n  readonly low: number;\n}\n\n/** Synthesis output for a single topic cluster. */\nexport interface ClusterSynthesis {\n  readonly topic: string;\n  readonly paperCount: number;\n  readonly papers: readonly string[];\n  readonly commonThemes: readonly string[];\n  readonly keyInsights: readonly string[];\n  readonly techniques: readonly string[];\n  readonly implementationOpportunities: readonly string[];\n  readonly gaps: readonly string[];\n  readonly alignedTechniques: readonly TechniqueAlignment[];\n  readonly qualityDistribution: QualityDistribution;\n}\n\n/** Summary of alignment between research and implementation. */\nexport interface AlignmentSummary {\n  readonly implemented: number;\n  readonly partial: number;\n  readonly notStarted: number;\n  readonly total: number;\n  readonly topOpportunities: readonly string[];\n}\n\n/** Summary of a single feature gate for synthesis output. */\nexport interface FeatureGateStatus {\n  readonly envVar: string;\n  readonly defaultValue: string;\n  readonly description: string;\n  readonly linkedTechniqueCount: number;\n}\n\n/** Full synthesis result across all clusters. */\nexport interface SynthesisResult {\n  readonly clusters: readonly ClusterSynthesis[];\n  readonly totalPapers: number;\n  readonly topicCount: number;\n  readonly crossCuttingThemes: readonly string[];\n  readonly alignmentSummary: AlignmentSummary;\n  readonly featureGates: readonly FeatureGateStatus[];\n}\n\n/** Error for synthesis operations. */\nexport interface SynthesisError {\n  readonly code: 'LOAD_ERROR' | 'NO_PAPERS';\n  readonly message: string;\n}\n\n// =============================================================================\n// CONSTANTS\n// =============================================================================\n\n/** Minimum papers in a cluster to generate cross-cutting themes. */\nconst MIN_CROSS_CUTTING_CLUSTER_SIZE = 2;\n\n/** Tags that appear across many topics and indicate cross-cutting themes. */\nconst CROSS_CUTTING_TAG_THRESHOLD = 3;\n\n// =============================================================================\n// PUBLIC API\n// =============================================================================\n\n/**\n * Synthesize the research registry by grouping papers into topic clusters\n * and generating structured summaries.\n *\n * @param topicFilter - Optional topic to filter to a single cluster\n * @returns Structured synthesis result\n */\nexport async function synthesizeResearch(\n  topicFilter?: string\n): Promise<Result<SynthesisResult, SynthesisError>> {\n  const registryResult = await loadPapersRegistry();\n  if (!registryResult.ok) {\n    return {\n      ok: false,\n      error: {\n        code: 'LOAD_ERROR',\n        message: `Failed to load papers: ${getErrorMessage(registryResult.error)}`,\n      },\n    };\n  }\n\n  const papers = extractPapers(registryResult.value);\n  if (papers.length === 0) {\n    return {\n      ok: false,\n      error: { code: 'NO_PAPERS', message: 'No papers found in registry' },\n    };\n  }\n\n  const clusters = groupByTopic(papers);\n  const filtered =\n    topicFilter !== undefined ? clusters.filter((c) => c.topic === topicFilter) : clusters;\n\n  const syntheses = filtered.map(synthesizeCluster);\n  const crossCutting = findCrossCuttingThemes(filtered);\n  const alignmentSummary = buildAlignmentSummary(syntheses);\n  const featureGates = buildFeatureGateSummary();\n\n  return {\n    ok: true,\n    value: {\n      clusters: syntheses,\n      totalPapers: papers.length,\n      topicCount: filtered.length,\n      crossCuttingThemes: crossCutting,\n      alignmentSummary,\n      featureGates,\n    },\n  };\n}\n\n// =============================================================================\n// EXTRACTION\n// =============================================================================\n\n/**\n * Safely convert a field that types say is `readonly string[]` but may be\n * null/undefined at runtime (YAML parsing of empty array fields).\n */\nfunction safeArray(value: readonly string[]): string[] {\n  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition -- YAML parsing can yield null despite type\n  if (value === null || value === undefined) return [];\n  return Array.from(value);\n}\n\n/** Extract papers from the registry structure. */\nfunction extractPapers(registry: PapersRegistry): SynthesisPaper[] {\n  return Object.entries(registry.papers).map(([id, p]) => ({\n    id,\n    title: p.title,\n    topics: safeArray(p.topics),\n    tags: safeArray(p.tags),\n    summary: p.summary.trim(),\n    keyFindings: safeArray(p.key_findings),\n    relevance: p.relevance,\n    implementationStatus: p.implementation_status,\n    techniquesExtracted: safeArray(p.techniques_extracted),\n    qualityScore: p.quality_score ?? 0,\n    evidenceTier: p.evidence_tier ?? 'low',\n  }));\n}\n\n// =============================================================================\n// GROUPING\n// =============================================================================\n\n/** Group papers by primary topic into clusters, normalizing free-form topics. */\nfunction groupByTopic(papers: readonly SynthesisPaper[]): PaperCluster[] {\n  const topicMap = new Map<string, SynthesisPaper[]>();\n\n  for (const paper of papers) {\n    for (const rawTopic of paper.topics) {\n      const topic = normalizeTopicToCanonical(rawTopic);\n      const existing = topicMap.get(topic);\n      if (existing !== undefined) {\n        existing.push(paper);\n      } else {\n        topicMap.set(topic, [paper]);\n      }\n    }\n  }\n\n  const clusters: PaperCluster[] = [];\n  for (const [topic, unsortedPapers] of topicMap) {\n    // Sort papers within cluster by quality_score descending (high-quality first)\n    const topicPapers = [...unsortedPapers].sort((a, b) => b.qualityScore - a.qualityScore);\n    clusters.push({\n      topic,\n      papers: topicPapers,\n      paperCount: topicPapers.length,\n    });\n  }\n\n  return clusters.sort((a, b) => b.paperCount - a.paperCount);\n}\n\n// =============================================================================\n// SYNTHESIS\n// =============================================================================\n\n/** Generate synthesis for a single topic cluster. */\n/** Compute quality score distribution for a set of papers. */\nfunction computeClusterQuality(papers: readonly SynthesisPaper[]): QualityDistribution {\n  const scores = papers.map((p) => p.qualityScore);\n  const totalScore = scores.reduce((sum, s) => sum + s, 0);\n  return {\n    avgScore: scores.length > 0 ? Math.round((totalScore / scores.length) * 10) / 10 : 0,\n    high: papers.filter((p) => p.evidenceTier === 'high').length,\n    medium: papers.filter((p) => p.evidenceTier === 'medium').length,\n    low: papers.filter((p) => p.evidenceTier === 'low').length,\n  };\n}\n\nfunction synthesizeCluster(cluster: PaperCluster): ClusterSynthesis {\n  const allTags = collectFrequencies(cluster.papers.flatMap((p) => [...p.tags]));\n  const allTechniques = collectFrequencies(\n    cluster.papers.flatMap((p) => [...p.techniquesExtracted])\n  );\n  const allFindings = cluster.papers.flatMap((p) => [...p.keyFindings]);\n\n  // Common themes: tags that appear in 2+ papers\n  const commonThemes = [...allTags.entries()]\n    .filter(([, count]) => count >= MIN_CROSS_CUTTING_CLUSTER_SIZE)\n    .sort((a, b) => b[1] - a[1])\n    .map(([tag]) => tag);\n\n  // Techniques across the cluster\n  const techniques = [...allTechniques.entries()]\n    .sort((a, b) => b[1] - a[1])\n    .map(([tech, count]) => (count > 1 ? `${tech} (${String(count)} papers)` : tech));\n\n  // Implementation opportunities: techniques not yet implemented\n  const notStarted = cluster.papers\n    .filter((p) => p.implementationStatus === 'not-started')\n    .flatMap((p) => [...p.techniquesExtracted]);\n  const uniqueOpportunities = [...new Set(notStarted)];\n\n  // Gaps: topics with few papers or missing techniques\n  const gaps: string[] = [];\n  if (cluster.paperCount === 1) {\n    gaps.push(`Only 1 paper — more research needed on ${cluster.topic}`);\n  }\n  const highRelevanceUnimplemented = cluster.papers.filter(\n    (p) => p.relevance === 'high' && p.implementationStatus === 'not-started'\n  );\n  if (highRelevanceUnimplemented.length > 0) {\n    gaps.push(\n      `${String(highRelevanceUnimplemented.length)} high-relevance paper(s) not yet implemented`\n    );\n  }\n\n  // Alignment analysis: map techniques to existing implementations\n  const allTechNames = [...allTechniques.keys()];\n  const alignedTechniques = analyzeClusterAlignment(allTechNames);\n\n  const qualityDistribution = computeClusterQuality(cluster.papers);\n\n  // Add quality gap if most papers are low-quality\n  if (qualityDistribution.low > qualityDistribution.high + qualityDistribution.medium) {\n    gaps.push(\n      `Mostly low-evidence papers (${String(qualityDistribution.low)}/${String(cluster.paperCount)}) — findings need stronger validation`\n    );\n  }\n\n  return {\n    topic: cluster.topic,\n    paperCount: cluster.paperCount,\n    papers: cluster.papers.map((p) => p.title),\n    commonThemes,\n    keyInsights: deduplicateFindings(allFindings).slice(0, 10),\n    techniques,\n    implementationOpportunities: uniqueOpportunities,\n    gaps,\n    alignedTechniques,\n    qualityDistribution,\n  };\n}\n\n/** Find themes that span multiple topic clusters. */\nfunction findCrossCuttingThemes(clusters: readonly PaperCluster[]): string[] {\n  const tagToTopics = new Map<string, Set<string>>();\n\n  for (const cluster of clusters) {\n    for (const paper of cluster.papers) {\n      for (const tag of paper.tags) {\n        const existing = tagToTopics.get(tag);\n        if (existing !== undefined) {\n          existing.add(cluster.topic);\n        } else {\n          tagToTopics.set(tag, new Set([cluster.topic]));\n        }\n      }\n    }\n  }\n\n  return [...tagToTopics.entries()]\n    .filter(([, topics]) => topics.size >= CROSS_CUTTING_TAG_THRESHOLD)\n    .sort((a, b) => b[1].size - a[1].size)\n    .map(([tag, topics]) => `${tag} (spans: ${[...topics].join(', ')})`);\n}\n\n// =============================================================================\n// ALIGNMENT ANALYSIS\n// =============================================================================\n\n/** Analyze technique alignment for a cluster. */\nfunction analyzeClusterAlignment(techniques: readonly string[]): TechniqueAlignment[] {\n  const alignments: TechniqueAlignment[] = [];\n\n  for (const tech of techniques) {\n    // Strip count annotation like \"technique (2 papers)\"\n    const baseTech = tech.replace(/\\s*\\(\\d+\\s*papers?\\)$/, '');\n    const mapping = TECHNIQUE_IMPLEMENTATION_MAP.get(baseTech);\n\n    if (mapping !== undefined) {\n      alignments.push({\n        technique: baseTech,\n        status: mapping.status,\n        canonicalPath: mapping.path,\n        ...(mapping.hint !== undefined ? { improvementHint: mapping.hint } : {}),\n      });\n    } else {\n      alignments.push({ technique: baseTech, status: 'not-started' });\n    }\n  }\n\n  return alignments;\n}\n\n/** Build alignment summary across all clusters. */\nfunction buildAlignmentSummary(clusters: readonly ClusterSynthesis[]): AlignmentSummary {\n  const allAlignments = clusters.flatMap((c) => c.alignedTechniques);\n  const implemented = allAlignments.filter((a) => a.status === 'implemented').length;\n  const partial = allAlignments.filter((a) => a.status === 'partial').length;\n  const notStarted = allAlignments.filter((a) => a.status === 'not-started').length;\n\n  // Top opportunities: partial implementations with hints (most improvable)\n  const opportunities = allAlignments\n    .filter((a) => a.status === 'partial' && a.improvementHint !== undefined)\n    .map((a) => `${a.technique}: ${a.improvementHint ?? ''}`)\n    .slice(0, 10);\n\n  return {\n    implemented,\n    partial,\n    notStarted,\n    total: allAlignments.length,\n    topOpportunities: opportunities,\n  };\n}\n\n/** Build feature gate summary from the inventory. */\nfunction buildFeatureGateSummary(): FeatureGateStatus[] {\n  return FEATURE_GATE_INVENTORY.map((g) => ({\n    envVar: g.envVar,\n    defaultValue: g.defaultValue,\n    description: g.description,\n    linkedTechniqueCount: g.techniques?.length ?? 0,\n  }));\n}\n\n// =============================================================================\n// UTILITIES\n// =============================================================================\n\nfunction collectFrequencies(items: readonly string[]): Map<string, number> {\n  const counts = new Map<string, number>();\n  for (const item of items) {\n    counts.set(item, (counts.get(item) ?? 0) + 1);\n  }\n  return counts;\n}\n\n/** Deduplicate findings by removing near-identical strings. */\nfunction deduplicateFindings(findings: readonly string[]): string[] {\n  const seen = new Set<string>();\n  const result: string[] = [];\n  for (const finding of findings) {\n    const normalized = finding.toLowerCase().trim();\n    if (normalized.length === 0) continue;\n    if (seen.has(normalized)) continue;\n    seen.add(normalized);\n    result.push(finding);\n  }\n  return 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