nexus-agents 2.26.1 → 2.28.0

package/dist/chunk-PGNRXCYY.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/mcp/tools/weather-report-types.ts","../src/mcp/gateway/gateway-keywords.ts","../src/mcp/gateway/tier-classifier.ts","../src/mcp/gateway/tier-recommender.ts","../src/adapters/rate-limit-detector.ts","../src/mcp/middleware/tool-metrics.ts","../src/agents/heartbeat-monitor.ts","../src/mcp/tools/weather-report.ts"],"sourcesContent":["/**\n * Type definitions for the Weather Report MCP tool.\n *\n * Surfaces observed model performance as a living \"weather report\"\n * and computes adaptive routing bonuses from outcome data.\n *\n * @module mcp/tools/weather-report-types\n * (Source: Issue #865 — Weather report with adaptive routing)\n */\n\nimport { z } from 'zod';\nimport type { TaskCategory } from '../../config/task-specialization-types.js';\nimport type { GroupStats } from '../../orchestration/outcomes/outcome-types.js';\nimport { CLI_NAMES, type CliNameLiteral } from '../../config/model-capabilities-types.js';\n\n// ============================================================================\n// Input Schema\n// ============================================================================\n\nexport const WeatherReportInputSchema = z.object({\n  /** Filter by CLI name. */\n  cli: z.enum(CLI_NAMES).optional().describe('Filter by CLI'),\n  /** Filter by task category. */\n  category: z\n    .enum([\n      'architecture',\n      'code_generation',\n      'code_review',\n      'research',\n      'security_review',\n      'planning',\n      'documentation',\n      'testing',\n      'devops',\n      'exploration',\n    ])\n    .optional()\n    .describe('Filter by task category'),\n  /** Include adaptive routing bonus data. */\n  includeAdaptive: z\n    .boolean()\n    .optional()\n    .default(true)\n    .describe('Include adaptive routing bonuses (default: true)'),\n});\n\n/** Validated MCP input (includeAdaptive is always populated after Zod parse). */\nexport type WeatherReportInput = z.infer<typeof WeatherReportInputSchema>;\n\n/** Options for generateWeatherReport (all fields optional). */\nexport interface WeatherReportOptions {\n  readonly cli?: CliNameLiteral;\n  readonly category?: string;\n  readonly includeAdaptive?: boolean;\n}\n\n// ============================================================================\n// Output Types\n// ============================================================================\n\n/** Per-CLI performance stats in the weather report. */\nexport interface CliWeather {\n  readonly cli: string;\n  readonly totalTasks: number;\n  readonly successRate: number;\n  readonly avgDurationMs: number;\n  readonly byCategory: ReadonlyMap<string, GroupStats>;\n}\n\n/** Adaptive bonus for a CLI+category pair. */\nexport interface AdaptiveBonus {\n  readonly cli: string;\n  readonly category: TaskCategory;\n  readonly staticBonus: number;\n  readonly adaptiveBonus: number;\n  readonly sampleCount: number;\n  readonly sufficient: boolean;\n}\n\n/** Tier recommendation surfaced in the weather report (#895). */\nexport interface TierRecommendationEntry {\n  readonly category: string;\n  readonly direction: 'promote' | 'demote';\n  readonly currentTier: number;\n  readonly recommendedTier: number;\n  readonly successRate: number;\n  readonly sampleCount: number;\n  readonly reason: string;\n}\n\n/** Learning insight for a CLI+category pair (Issue #901, Phase 4). */\nexport interface LearningInsight {\n  readonly cli: string;\n  readonly category: TaskCategory;\n  readonly trend: 'improving' | 'declining' | 'stable';\n  readonly confidence: number;\n  readonly adjustedBaseline: number;\n  readonly sampleCount: number;\n}\n\n/** Recommended CLI→category mapping for LinUCB cold-start (Epic #952, Phase 6). */\nexport interface RecommendedMapping {\n  readonly category: TaskCategory;\n  readonly recommendedCli: string;\n  readonly successRate: number;\n  readonly sampleCount: number;\n  readonly confidence: 'high' | 'medium' | 'low';\n}\n\n/** Rate limit stats per provider (Issue #996). */\nexport interface RateLimitReport {\n  readonly provider: string;\n  readonly totalHits: number;\n  readonly lastHitAt: number;\n  readonly avgRetryAfterMs: number | undefined;\n}\n\n/** Per-tool performance stats (Issue #1022). */\nexport interface ToolPerformanceEntry {\n  readonly toolName: string;\n  readonly totalCalls: number;\n  readonly successRate: number;\n  readonly avgDurationMs: number;\n  readonly errorCount: number;\n}\n\n/** Failure breakdown entry for the weather report (Issue #1025). */\nexport interface FailureBreakdownEntry {\n  readonly category: string;\n  readonly count: number;\n  readonly percentage: number;\n}\n\n/** Per-expert-role performance stats from worker dispatch outcomes (Issue #1324). */\nexport interface ExpertPerformanceEntry {\n  readonly role: string;\n  readonly totalTasks: number;\n  readonly successRate: number;\n  readonly avgDurationMs: number;\n  readonly dominantErrorPattern?: string;\n}\n\n/** Agent health summary from heartbeat monitor (Issue #1032). */\nexport interface AgentHealthSummary {\n  readonly activeSessions: number;\n  readonly stalledSessions: number;\n  readonly sessions: readonly AgentSessionEntry[];\n}\n\n/** Single agent session health entry. */\nexport interface AgentSessionEntry {\n  readonly sessionId: string;\n  readonly expertId: string;\n  readonly health: 'alive' | 'slow' | 'stalled';\n  readonly elapsedMs: number;\n  readonly timeSinceHeartbeatMs: number;\n  readonly heartbeatCount: number;\n}\n\n/** Full weather report response. */\nexport interface WeatherReportResponse {\n  readonly overall: {\n    readonly totalTasks: number;\n    readonly successRate: number;\n    readonly avgDurationMs: number;\n  };\n  readonly cliWeather: readonly CliWeather[];\n  readonly adaptiveBonuses: readonly AdaptiveBonus[];\n  /** Outcome-driven tier change recommendations (#895). */\n  readonly tierRecommendations: readonly TierRecommendationEntry[];\n  /** Adaptive learning insights per CLI+category (#901). */\n  readonly learningInsights?: readonly LearningInsight[];\n  /** Recommended CLI mappings per category for LinUCB priors (Epic #952). */\n  readonly recommendedMappings?: readonly RecommendedMapping[];\n  /** Rate limit utilization per provider (Issue #996). */\n  readonly rateLimits?: readonly RateLimitReport[];\n  /** Per-tool invocation metrics (Issue #1022). */\n  readonly toolPerformance?: readonly ToolPerformanceEntry[];\n  /** Failure breakdown by category (Issue #1025). */\n  readonly failureBreakdown?: readonly FailureBreakdownEntry[];\n  /** Agent health from heartbeat monitor (Issue #1032). */\n  readonly agentHealth?: AgentHealthSummary;\n  /** Per-expert-role performance from worker dispatch outcomes (Issue #1324). */\n  readonly expertPerformance?: readonly ExpertPerformanceEntry[];\n  readonly explorationRate: number;\n  readonly coldStartThreshold: number;\n  readonly collectedAt: string;\n}\n\n// ============================================================================\n// Configuration\n// ============================================================================\n\nexport const WeatherReportConfigSchema = z.object({\n  /** Minimum observations before adjusting bonuses (lowered for faster activation). */\n  coldStartThreshold: z.number().int().min(1).max(1000).default(3),\n  /** Exploration rate: fraction of random routing (0.0-1.0). */\n  explorationRate: z.number().min(0).max(1).default(0.1),\n  /** Max adaptive bonus adjustment (+/-). */\n  maxBonusAdjustment: z.number().min(0).max(10).default(5),\n});\n\nexport type WeatherReportConfig = z.infer<typeof WeatherReportConfigSchema>;\n\n/** Creates default configuration. */\nexport function createDefaultWeatherConfig(): WeatherReportConfig {\n  return WeatherReportConfigSchema.parse({});\n}\n","/**\n * Gateway Keyword Constants\n *\n * Single source of truth for security and architecture keywords used by\n * both the tier classifier and governance enforcer. Extracted to prevent\n * divergence between the two modules (DRY).\n *\n * @module mcp/gateway/gateway-keywords\n */\n\n/** Keywords that indicate security-related work (case-insensitive substring match). */\nexport const SECURITY_KEYWORDS = [\n  'security',\n  'vulnerabilit',\n  'cve-',\n  'exploit',\n  'injection',\n  'xss',\n  'csrf',\n  'auth',\n  'penetration',\n  'threat',\n  'malware',\n  'credentials',\n  'secrets',\n  'encryption',\n  'certificate',\n] as const;\n\n/** Keywords that indicate architecture-related work (case-insensitive substring match). */\nexport const ARCHITECTURE_KEYWORDS = [\n  'architecture',\n  'breaking change',\n  'breaking api',\n  'api change',\n  'migration',\n  'refactor.*system',\n  'redesign',\n  'microservice',\n  'monolith',\n  'deprecation',\n  'schema change',\n  'database',\n  'infrastructure',\n] as const;\n\n/** Roles that always trigger promotion to Tier 3. */\nexport const PROMOTED_ROLES = new Set(['security_expert', 'architecture_expert']);\n","/**\n * Request Tier Classifier\n *\n * Pure function that classifies incoming MCP tool requests into tiers\n * for the orchestration gateway. No side effects, no I/O.\n *\n * Tier 1 (DIRECT):       Read-only tools — direct dispatch + logging\n * Tier 2 (ANALYZED):     Model-selection tools — task analysis first\n * Tier 3 (ORCHESTRATED): Complex/risky tools — full orchestration pipeline\n *\n * Security and architecture-related requests are always promoted to Tier 3.\n *\n * @module mcp/gateway/tier-classifier\n * (Source: Issue #892, Epic #888)\n */\n\nimport { SECURITY_KEYWORDS, ARCHITECTURE_KEYWORDS, PROMOTED_ROLES } from './gateway-keywords.js';\n\n/** Request processing tier. Higher = more orchestration overhead. */\nexport enum RequestTier {\n  /** Direct dispatch with structured logging. */\n  DIRECT = 1,\n  /** Task analysis + model selection via delegate_to_model. */\n  ANALYZED = 2,\n  /** Full orchestration + decomposition + voting. */\n  ORCHESTRATED = 3,\n}\n\n/** Per-tool tier override map (from nexus-agents.yaml). */\nexport type TierOverrides = Record<string, RequestTier>;\n\n/**\n * Default tier assignment for all 20 registered MCP tools.\n * Tier 1: read-only, no model invocation needed.\n * Tier 2: requires model selection or expert creation.\n * Tier 3: requires full orchestration, decomposition, or consensus.\n */\nexport const TOOL_TIER_MAP: Readonly<Record<string, RequestTier>> = {\n  // Tier 1 — Read-only\n  list_experts: RequestTier.DIRECT,\n  list_workflows: RequestTier.DIRECT,\n  memory_query: RequestTier.DIRECT,\n  memory_stats: RequestTier.DIRECT,\n  weather_report: RequestTier.DIRECT,\n  research_query: RequestTier.DIRECT,\n  research_analyze: RequestTier.DIRECT,\n  research_catalog_review: RequestTier.DIRECT,\n\n  // Tier 2 — Model selection\n  delegate_to_model: RequestTier.ANALYZED,\n  create_expert: RequestTier.ANALYZED,\n  execute_expert: RequestTier.ANALYZED,\n  research_add: RequestTier.ANALYZED,\n  research_discover: RequestTier.ANALYZED,\n  registry_import: RequestTier.ANALYZED,\n\n  // Tier 3 — Full orchestration\n  orchestrate: RequestTier.ORCHESTRATED,\n  consensus_vote: RequestTier.ORCHESTRATED,\n  execute_spec: RequestTier.ORCHESTRATED,\n  run_workflow: RequestTier.ORCHESTRATED,\n  run_graph_workflow: RequestTier.ORCHESTRATED,\n  issue_triage: RequestTier.ORCHESTRATED,\n};\n\n/**\n * Classifies an MCP tool request into a processing tier.\n *\n * @param toolName - The MCP tool being invoked\n * @param params - The tool's input parameters\n * @param overrides - Optional per-tool tier overrides\n * @returns The appropriate RequestTier for this request\n */\nexport function classifyRequestTier(\n  toolName: string,\n  params: Record<string, unknown>,\n  overrides?: TierOverrides\n): RequestTier {\n  const defaultTier = TOOL_TIER_MAP[toolName] ?? RequestTier.ANALYZED;\n  const effectiveTier = overrides?.[toolName] ?? defaultTier;\n\n  // Tier 1 tools (from canonical map, not overridden) skip promotion checks\n  if (defaultTier === RequestTier.DIRECT && effectiveTier === RequestTier.DIRECT) {\n    return RequestTier.DIRECT;\n  }\n\n  // Security/architecture promotion always wins — overrides cannot suppress it\n  if (effectiveTier < RequestTier.ORCHESTRATED && shouldPromote(params)) {\n    return RequestTier.ORCHESTRATED;\n  }\n\n  return effectiveTier;\n}\n\n/**\n * Checks if request params contain security or architecture keywords\n * that warrant promotion to Tier 3.\n */\nfunction shouldPromote(params: Record<string, unknown>): boolean {\n  // Check role-based promotion\n  const role = params['role'];\n  if (typeof role === 'string' && PROMOTED_ROLES.has(role)) {\n    return true;\n  }\n\n  // Check text content for keyword matches\n  const textFields = ['task', 'proposal', 'prompt'];\n  for (const field of textFields) {\n    const value = params[field];\n    if (typeof value === 'string' && containsPromotionKeyword(value)) {\n      return true;\n    }\n  }\n\n  return false;\n}\n\n/** Map from config string tier names to RequestTier enum values. */\nconst TIER_NAME_TO_ENUM: Readonly<Record<string, RequestTier>> = {\n  DIRECT: RequestTier.DIRECT,\n  ANALYZED: RequestTier.ANALYZED,\n  ORCHESTRATED: RequestTier.ORCHESTRATED,\n};\n\n/**\n * Converts string tier override map (from config schema) to RequestTier enum map.\n * Ignores entries with invalid tier names.\n *\n * @param overrides - String-keyed tier names from GatewayConfigSchema\n * @returns Enum-valued TierOverrides, or undefined if empty/undefined\n */\nexport function parseTierOverrides(\n  overrides: Record<string, string> | undefined\n): TierOverrides | undefined {\n  if (overrides === undefined) return undefined;\n  const result: TierOverrides = {};\n  for (const [tool, tierName] of Object.entries(overrides)) {\n    const tier = TIER_NAME_TO_ENUM[tierName];\n    if (tier !== undefined) {\n      result[tool] = tier;\n    }\n  }\n  return Object.keys(result).length > 0 ? result : undefined;\n}\n\n/** Checks if text contains any security or architecture promotion keyword. */\nfunction containsPromotionKeyword(text: string): boolean {\n  const lower = text.toLowerCase();\n  for (const kw of SECURITY_KEYWORDS) {\n    if (lower.includes(kw)) return true;\n  }\n  for (const kw of ARCHITECTURE_KEYWORDS) {\n    if (new RegExp(kw, 'i').test(text)) return true;\n  }\n  return false;\n}\n","/**\n * Outcome-Driven Tier Promotion Recommender\n *\n * Analyzes task outcome data to recommend tier changes for MCP tools.\n * Recommendations are advisory only — humans approve changes via config.\n *\n * Thresholds (from Issue #895):\n * - Promote: >30% failure rate at current tier → recommend next tier\n * - Demote:  >95% success rate over 50+ executions → eligible for demotion\n * - Minimum sample: 20 executions before any recommendation\n *\n * @module mcp/gateway/tier-recommender\n * (Source: Issue #895, Epic #888)\n */\n\nimport type { PerformanceSummary, GroupStats } from '../../orchestration/outcomes/outcome-types.js';\nimport { RequestTier, TOOL_TIER_MAP } from './tier-classifier.js';\n\n/** Recommendation direction. */\nexport type TierDirection = 'promote' | 'demote';\n\n/** A single tier change recommendation. */\nexport interface TierRecommendation {\n  /** Category that triggered this recommendation. */\n  category: string;\n  /** Current tier for tools in this category. */\n  currentTier: RequestTier;\n  /** Recommended tier. */\n  recommendedTier: RequestTier;\n  /** Direction of the recommendation. */\n  direction: TierDirection;\n  /** Observed success rate (0-1). */\n  successRate: number;\n  /** Number of observations. */\n  sampleCount: number;\n  /** Human-readable reason. */\n  reason: string;\n}\n\n/** Configuration for tier recommendation thresholds. */\nexport interface TierRecommenderConfig {\n  /** Minimum executions before making any recommendation. */\n  readonly minSamples: number;\n  /** Failure rate threshold for promotion (0-1). */\n  readonly promoteFailureRate: number;\n  /** Success rate threshold for demotion (0-1). */\n  readonly demoteSuccessRate: number;\n  /** Minimum executions for demotion eligibility. */\n  readonly demoteMinSamples: number;\n}\n\n/** Default configuration per issue spec. */\nconst DEFAULT_CONFIG: TierRecommenderConfig = {\n  minSamples: 20,\n  promoteFailureRate: 0.3,\n  demoteSuccessRate: 0.95,\n  demoteMinSamples: 50,\n};\n\n/** Maps categories to their typical tool tier (best effort). */\nfunction getCategoryTier(category: string): RequestTier {\n  // Tools that tend to be used for each category\n  const categoryToolMap: Record<string, string> = {\n    research: 'research_query',\n    exploration: 'research_discover',\n    code_generation: 'delegate_to_model',\n    code_review: 'run_workflow',\n    architecture: 'orchestrate',\n    security_review: 'orchestrate',\n    planning: 'orchestrate',\n    documentation: 'run_workflow',\n    testing: 'run_workflow',\n    devops: 'delegate_to_model',\n  };\n\n  const tool = categoryToolMap[category];\n  if (tool !== undefined) {\n    return TOOL_TIER_MAP[tool] ?? RequestTier.ANALYZED;\n  }\n  return RequestTier.ANALYZED;\n}\n\n/**\n * Generates tier recommendations from outcome data.\n *\n * @param summary - Performance summary from OutcomeStore.summarize()\n * @param config - Optional threshold overrides\n * @returns Array of tier change recommendations (may be empty)\n */\nexport function generateTierRecommendations(\n  summary: PerformanceSummary,\n  config?: Partial<TierRecommenderConfig>\n): TierRecommendation[] {\n  const cfg = { ...DEFAULT_CONFIG, ...config };\n  const recommendations: TierRecommendation[] = [];\n\n  for (const [category, stats] of summary.byCategory) {\n    const rec = evaluateCategory(category, stats, cfg);\n    if (rec !== null) recommendations.push(rec);\n  }\n\n  return recommendations;\n}\n\n/** Evaluates a single category for promotion or demotion. */\nfunction evaluateCategory(\n  category: string,\n  stats: GroupStats,\n  cfg: TierRecommenderConfig\n): TierRecommendation | null {\n  if (stats.count < cfg.minSamples) return null;\n\n  const currentTier = getCategoryTier(category);\n  const failureRate = 1 - stats.successRate;\n\n  // Check for promotion (too many failures at current tier)\n  if (failureRate > cfg.promoteFailureRate && currentTier < RequestTier.ORCHESTRATED) {\n    const recommendedTier = currentTier + 1;\n    return {\n      category,\n      currentTier,\n      recommendedTier,\n      direction: 'promote',\n      successRate: stats.successRate,\n      sampleCount: stats.count,\n      reason: `${category}: ${(failureRate * 100).toFixed(0)}% failure rate over ${String(stats.count)} tasks — recommend promoting to Tier ${String(recommendedTier)}`,\n    };\n  }\n\n  // Check for demotion (consistently successful at current tier)\n  if (\n    stats.successRate > cfg.demoteSuccessRate &&\n    stats.count >= cfg.demoteMinSamples &&\n    currentTier > RequestTier.DIRECT\n  ) {\n    const recommendedTier = currentTier - 1;\n    return {\n      category,\n      currentTier,\n      recommendedTier,\n      direction: 'demote',\n      successRate: stats.successRate,\n      sampleCount: stats.count,\n      reason: `${category}: ${(stats.successRate * 100).toFixed(0)}% success rate over ${String(stats.count)} tasks — eligible for demotion to Tier ${String(recommendedTier)}`,\n    };\n  }\n\n  return null;\n}\n","/**\n * Rate Limit Detection and Tracking\n *\n * Detects rate limit errors from model adapter responses and tracks\n * rate limit events for weather report metrics.\n *\n * @module adapters/rate-limit-detector\n * (Source: Issue #996 — Rate limit error surfacing)\n */\n\nimport { RateLimitError, getErrorMessage } from '../core/index.js';\n\n// ============================================================================\n// Detection\n// ============================================================================\n\nconst RATE_LIMIT_PATTERNS = [\n  'rate limit',\n  'rate_limit',\n  'too many requests',\n  '429',\n  'quota exceeded',\n  'throttl',\n  'requests per minute',\n  'tokens per minute',\n] as const;\n\n/**\n * Detects whether an error is a rate limit error.\n * Pattern-matches against common provider error messages.\n */\nexport function isRateLimitLikeError(error: unknown): boolean {\n  const message = getErrorMessage(error).toLowerCase();\n  return RATE_LIMIT_PATTERNS.some((p) => message.includes(p));\n}\n\n/**\n * Parses retry-after metadata from an error message.\n * Providers often include timing hints in error messages.\n */\nexport function parseRetryAfterMs(errorMessage: string): number | undefined {\n  const lower = errorMessage.toLowerCase();\n\n  // Match \"retry after X seconds\" or \"retry-after: X\"\n  const secondsMatch = /retry[- ]?after[:\\s]+(\\d+(?:\\.\\d+)?)\\s*(?:s|sec)/i.exec(lower);\n  if (secondsMatch !== null) {\n    const parsed = parseFloat(secondsMatch[1] ?? '0');\n    return Math.ceil(parsed * 1000);\n  }\n\n  // Match \"retry after X ms\" or \"wait X milliseconds\"\n  const msMatch = /(?:retry[- ]?after|wait)[:\\s]+(\\d+)\\s*(?:ms|millisecond)/i.exec(lower);\n  if (msMatch !== null) {\n    return parseInt(msMatch[1] ?? '0', 10);\n  }\n\n  // Match \"try again in X seconds\"\n  const againMatch = /try again in (\\d+(?:\\.\\d+)?)\\s*(?:s|sec)/i.exec(lower);\n  if (againMatch !== null) {\n    const parsed = parseFloat(againMatch[1] ?? '0');\n    return Math.ceil(parsed * 1000);\n  }\n\n  return undefined;\n}\n\n/**\n * Wraps a generic error as a RateLimitError with parsed metadata.\n */\nexport function toRateLimitError(error: unknown, provider?: string): RateLimitError {\n  const message = getErrorMessage(error);\n  const retryAfterMs = parseRetryAfterMs(message);\n  return new RateLimitError(message, {\n    ...(retryAfterMs !== undefined ? { retryAfterMs } : {}),\n    ...(provider !== undefined ? { provider } : {}),\n    ...(error instanceof Error ? { cause: error } : {}),\n  });\n}\n\n// ============================================================================\n// Tracking\n// ============================================================================\n\n/** A single rate limit event record. */\nexport interface RateLimitEvent {\n  readonly provider: string;\n  readonly timestamp: number;\n  readonly retryAfterMs: number | undefined;\n}\n\n/** Aggregate stats for rate limit events per provider. */\nexport interface RateLimitStats {\n  readonly provider: string;\n  readonly totalHits: number;\n  readonly lastHitAt: number;\n  readonly avgRetryAfterMs: number | undefined;\n}\n\nconst MAX_EVENTS = 200;\nconst events: RateLimitEvent[] = [];\n\n/** Records a rate limit event for tracking. */\nexport function recordRateLimitEvent(event: RateLimitEvent): void {\n  events.push(event);\n  if (events.length > MAX_EVENTS) {\n    events.splice(0, events.length - MAX_EVENTS);\n  }\n}\n\n/** Gets rate limit stats grouped by provider. */\nexport function getRateLimitStats(): readonly RateLimitStats[] {\n  const grouped = new Map<string, RateLimitEvent[]>();\n  for (const event of events) {\n    const existing = grouped.get(event.provider);\n    if (existing !== undefined) {\n      existing.push(event);\n    } else {\n      grouped.set(event.provider, [event]);\n    }\n  }\n\n  const stats: RateLimitStats[] = [];\n  for (const [provider, providerEvents] of grouped) {\n    const retryValues = providerEvents\n      .map((e) => e.retryAfterMs)\n      .filter((v): v is number => v !== undefined);\n    const avgRetry =\n      retryValues.length > 0\n        ? retryValues.reduce((a, b) => a + b, 0) / retryValues.length\n        : undefined;\n    const lastEvent = providerEvents[providerEvents.length - 1];\n\n    stats.push({\n      provider,\n      totalHits: providerEvents.length,\n      lastHitAt: lastEvent?.timestamp ?? 0,\n      ...(avgRetry !== undefined\n        ? { avgRetryAfterMs: Math.round(avgRetry) }\n        : { avgRetryAfterMs: undefined }),\n    });\n  }\n\n  return stats;\n}\n\n/** Clears all tracked rate limit events. Useful for testing. */\nexport function clearRateLimitEvents(): void {\n  events.length = 0;\n}\n","/**\n * Tool usage metrics recorder (Issue #1022)\n *\n * Lightweight, bounded, in-memory store for MCP tool invocation metrics.\n * Records tool name, duration, and success/failure for every tool call.\n * Used by the weather report to surface per-tool analytics.\n *\n * @module mcp/middleware/tool-metrics\n */\n\nimport { getTimeProvider } from '../../core/index.js';\nimport type { Middleware, ToolResult } from './middleware-chain.js';\n\n// ============================================================================\n// Types\n// ============================================================================\n\n/** A single recorded tool invocation metric. */\nexport interface ToolMetric {\n  readonly toolName: string;\n  readonly durationMs: number;\n  readonly success: boolean;\n  readonly timestamp: string;\n}\n\n/** Aggregated stats for a single tool. */\nexport interface ToolStats {\n  readonly toolName: string;\n  readonly totalCalls: number;\n  readonly successRate: number;\n  readonly avgDurationMs: number;\n  readonly errorCount: number;\n}\n\n// ============================================================================\n// Store\n// ============================================================================\n\nconst MAX_ENTRIES = 5_000;\nconst metrics: ToolMetric[] = [];\n\n/** Record a tool invocation metric. */\nexport function recordToolMetric(metric: ToolMetric): void {\n  metrics.push(metric);\n  if (metrics.length > MAX_ENTRIES) {\n    metrics.splice(0, metrics.length - MAX_ENTRIES);\n  }\n}\n\n/** Get all recorded tool metrics (read-only snapshot). */\nexport function getToolMetrics(): readonly ToolMetric[] {\n  return [...metrics];\n}\n\n/** Aggregate metrics into per-tool stats. */\nexport function getToolStats(): readonly ToolStats[] {\n  const groups = new Map<string, ToolMetric[]>();\n\n  for (const m of metrics) {\n    const list = groups.get(m.toolName);\n    if (list !== undefined) {\n      list.push(m);\n    } else {\n      groups.set(m.toolName, [m]);\n    }\n  }\n\n  const stats: ToolStats[] = [];\n  for (const [toolName, list] of groups) {\n    const sc = list.filter((m) => m.success).length;\n    const td = list.reduce((s, m) => s + m.durationMs, 0);\n    stats.push({\n      toolName,\n      totalCalls: list.length,\n      successRate: sc / list.length,\n      avgDurationMs: td / list.length,\n      errorCount: list.length - sc,\n    });\n  }\n\n  return stats.sort((a, b) => b.totalCalls - a.totalCalls);\n}\n\n/** Clear all recorded metrics (for testing). */\nexport function clearToolMetrics(): void {\n  metrics.length = 0;\n}\n\n// ============================================================================\n// Middleware\n// ============================================================================\n\n/**\n * Creates a middleware that records tool invocation metrics.\n * Should be placed as the outermost middleware (before audit)\n * to capture the full request lifecycle including middleware overhead.\n */\nexport function createMetricsMiddleware(): Middleware {\n  return async (args, ctx, next): Promise<ToolResult> => {\n    const startTime = getTimeProvider().now();\n\n    try {\n      const result = await next(args, ctx);\n      const durationMs = getTimeProvider().now() - startTime;\n\n      recordToolMetric({\n        toolName: ctx.requestContext.toolName,\n        durationMs,\n        success: result.isError !== true,\n        timestamp: new Date().toISOString(),\n      });\n\n      return result;\n    } catch (error) {\n      const durationMs = getTimeProvider().now() - startTime;\n\n      recordToolMetric({\n        toolName: ctx.requestContext.toolName,\n        durationMs,\n        success: false,\n        timestamp: new Date().toISOString(),\n      });\n\n      throw error;\n    }\n  };\n}\n","/**\n * Heartbeat-based liveness monitor for expert agent sessions.\n *\n * Tracks active expert executions with periodic heartbeats.\n * Detects stalled sessions that stop making progress, enabling\n * faster detection than wall-clock timeouts alone.\n *\n * @module agents/heartbeat-monitor\n * (Source: Issue #1032 — Agent heartbeat health monitor)\n */\n\n// ============================================================================\n// Types\n// ============================================================================\n\n/** Health status of an expert session. */\nexport type SessionHealth = 'alive' | 'slow' | 'stalled';\n\n/** Snapshot of a single expert session. */\nexport interface ExpertSessionSnapshot {\n  readonly sessionId: string;\n  readonly expertId: string;\n  readonly startedAt: number;\n  readonly lastHeartbeat: number;\n  readonly heartbeatCount: number;\n  readonly health: SessionHealth;\n  readonly elapsedMs: number;\n  readonly timeSinceHeartbeatMs: number;\n}\n\n/** Aggregate health report for all active sessions. */\nexport interface AgentHealthReport {\n  readonly activeSessions: number;\n  readonly stalledSessions: number;\n  readonly sessions: readonly ExpertSessionSnapshot[];\n}\n\n/** Configuration for the heartbeat monitor. */\nexport interface HeartbeatConfig {\n  /** Time without heartbeat before marking 'slow' (ms). */\n  readonly slowThresholdMs: number;\n  /** Time without heartbeat before marking 'stalled' (ms). */\n  readonly stalledThresholdMs: number;\n  /** Absolute max lifetime for any session (ms). Safety cap. */\n  readonly absoluteMaxMs: number;\n}\n\n// ============================================================================\n// Constants\n// ============================================================================\n\n// Canonical source: config/timeouts.ts (Issue #1046)\nimport { HEARTBEAT_TIMEOUTS } from '../config/timeouts.js';\n\nconst DEFAULT_SLOW_THRESHOLD_MS = HEARTBEAT_TIMEOUTS.slowThresholdMs;\nconst DEFAULT_STALLED_THRESHOLD_MS = HEARTBEAT_TIMEOUTS.stalledThresholdMs;\nconst DEFAULT_ABSOLUTE_MAX_MS = HEARTBEAT_TIMEOUTS.absoluteMaxMs;\n\n// ============================================================================\n// Internal Session State\n// ============================================================================\n\ninterface SessionEntry {\n  readonly expertId: string;\n  readonly startedAt: number;\n  lastHeartbeat: number;\n  heartbeatCount: number;\n  /** Previous health state for transition detection (Issue #1088 Phase 4). */\n  previousHealth: SessionHealth;\n}\n\n/** Health transition info returned by getSessionHealth(). */\nexport interface HealthTransition {\n  readonly sessionId: string;\n  readonly agentId: string;\n  readonly health: SessionHealth;\n  readonly previousHealth: SessionHealth;\n  readonly changed: boolean;\n  readonly elapsedMs: number;\n  readonly heartbeatCount: number;\n}\n\n// ============================================================================\n// HeartbeatMonitor\n// ============================================================================\n\n/**\n * Tracks expert session liveness via heartbeats.\n *\n * - `startSession()` begins tracking a new expert execution\n * - `heartbeat()` resets the liveness timer for a session\n * - `endSession()` stops tracking\n * - `getHealth()` returns aggregate health report\n * - `isStalled()` checks if a specific session is stalled\n */\nexport class HeartbeatMonitor {\n  private readonly config: HeartbeatConfig;\n  private readonly sessions = new Map<string, SessionEntry>();\n\n  constructor(config?: Partial<HeartbeatConfig>) {\n    this.config = {\n      slowThresholdMs: config?.slowThresholdMs ?? DEFAULT_SLOW_THRESHOLD_MS,\n      stalledThresholdMs: config?.stalledThresholdMs ?? DEFAULT_STALLED_THRESHOLD_MS,\n      absoluteMaxMs: config?.absoluteMaxMs ?? DEFAULT_ABSOLUTE_MAX_MS,\n    };\n  }\n\n  /** Start tracking a new expert session. Returns session ID. */\n  startSession(expertId: string): string {\n    const sessionId = `hb-${expertId}-${String(Date.now())}`;\n    const now = Date.now();\n    this.sessions.set(sessionId, {\n      expertId,\n      startedAt: now,\n      lastHeartbeat: now,\n      heartbeatCount: 0,\n      previousHealth: 'alive',\n    });\n    return sessionId;\n  }\n\n  /** Record a heartbeat for an active session. */\n  heartbeat(sessionId: string): void {\n    const entry = this.sessions.get(sessionId);\n    if (entry === undefined) return;\n    entry.lastHeartbeat = Date.now();\n    entry.heartbeatCount++;\n  }\n\n  /** Stop tracking a session. */\n  endSession(sessionId: string): void {\n    this.sessions.delete(sessionId);\n  }\n\n  /** Check if a session has exceeded the stalled threshold. */\n  isStalled(sessionId: string): boolean {\n    const entry = this.sessions.get(sessionId);\n    if (entry === undefined) return false;\n    const elapsed = Date.now() - entry.lastHeartbeat;\n    return elapsed >= this.config.stalledThresholdMs;\n  }\n\n  /** Check if a session has exceeded the absolute max lifetime. */\n  isExpired(sessionId: string): boolean {\n    const entry = this.sessions.get(sessionId);\n    if (entry === undefined) return false;\n    return Date.now() - entry.startedAt >= this.config.absoluteMaxMs;\n  }\n\n  /** Get aggregate health report for all active sessions. */\n  getHealth(): AgentHealthReport {\n    const now = Date.now();\n    const sessions: ExpertSessionSnapshot[] = [];\n    let stalledCount = 0;\n\n    for (const [sessionId, entry] of this.sessions) {\n      const timeSince = now - entry.lastHeartbeat;\n      const health = this.classifyHealth(timeSince);\n      if (health === 'stalled') stalledCount++;\n\n      sessions.push({\n        sessionId,\n        expertId: entry.expertId,\n        startedAt: entry.startedAt,\n        lastHeartbeat: entry.lastHeartbeat,\n        heartbeatCount: entry.heartbeatCount,\n        health,\n        elapsedMs: now - entry.startedAt,\n        timeSinceHeartbeatMs: timeSince,\n      });\n    }\n\n    return {\n      activeSessions: this.sessions.size,\n      stalledSessions: stalledCount,\n      sessions,\n    };\n  }\n\n  /**\n   * Get health state with transition detection for a session.\n   * Updates previousHealth on each call to track transitions.\n   * (Issue #1088 Phase 4 — observability)\n   */\n  getSessionHealth(sessionId: string): HealthTransition | undefined {\n    const entry = this.sessions.get(sessionId);\n    if (entry === undefined) return undefined;\n    const now = Date.now();\n    const timeSince = now - entry.lastHeartbeat;\n    const health = this.classifyHealth(timeSince);\n    const changed = health !== entry.previousHealth;\n    const result: HealthTransition = {\n      sessionId,\n      agentId: entry.expertId,\n      health,\n      previousHealth: entry.previousHealth,\n      changed,\n      elapsedMs: now - entry.startedAt,\n      heartbeatCount: entry.heartbeatCount,\n    };\n    entry.previousHealth = health;\n    return result;\n  }\n\n  /** Number of currently tracked sessions. */\n  get activeCount(): number {\n    return this.sessions.size;\n  }\n\n  private classifyHealth(timeSinceMs: number): SessionHealth {\n    if (timeSinceMs >= this.config.stalledThresholdMs) return 'stalled';\n    if (timeSinceMs >= this.config.slowThresholdMs) return 'slow';\n    return 'alive';\n  }\n}\n\n// ============================================================================\n// Singleton\n// ============================================================================\n\nlet globalMonitor: HeartbeatMonitor | undefined;\n\n/** Get or create the global heartbeat monitor singleton. */\nexport function getHeartbeatMonitor(): HeartbeatMonitor {\n  globalMonitor ??= new HeartbeatMonitor();\n  return globalMonitor;\n}\n\n/** Reset global monitor (for testing). */\nexport function resetHeartbeatMonitor(): void {\n  globalMonitor = undefined;\n}\n","/**\n * nexus-agents/mcp - Weather Report\n *\n * Computes a living performance dashboard from task outcome data\n * and calculates adaptive routing bonuses using epsilon-greedy\n * exploration/exploitation tradeoff.\n *\n * @module mcp/tools/weather-report\n * (Source: Issue #865 — Weather report with adaptive routing)\n */\n\nimport type { PerformanceSummary, GroupStats } from '../../orchestration/outcomes/outcome-types.js';\nimport { getOutcomeStore } from '../../orchestration/outcomes/index.js';\nimport type { TaskCategory } from '../../config/task-specialization-types.js';\nimport { TASK_CATEGORIES } from '../../config/task-specialization-types.js';\nimport { getSpecialization } from '../../config/task-specialization.js';\nimport type { CliNameLiteral } from '../../config/model-capabilities-types.js';\nimport type {\n  WeatherReportOptions,\n  WeatherReportResponse,\n  CliWeather,\n  AdaptiveBonus,\n  WeatherReportConfig,\n  TierRecommendationEntry,\n  LearningInsight,\n  RecommendedMapping,\n  ToolPerformanceEntry,\n  FailureBreakdownEntry,\n  ExpertPerformanceEntry,\n} from './weather-report-types.js';\nimport type { RateLimitReport } from './weather-report-types.js';\nimport { createDefaultWeatherConfig } from './weather-report-types.js';\nimport { generateTierRecommendations } from '../gateway/tier-recommender.js';\nimport { computeAdaptiveThresholds } from '../../orchestration/outcomes/adaptive-thresholds.js';\nimport { getRateLimitStats } from '../../adapters/rate-limit-detector.js';\nimport { getToolStats } from '../middleware/tool-metrics.js';\nimport { getHeartbeatMonitor } from '../../agents/heartbeat-monitor.js';\nimport type { AgentHealthSummary } from './weather-report-types.js';\n\n// ============================================================================\n// Public API\n// ============================================================================\n\nconst CLI_NAMES = ['claude', 'gemini', 'codex', 'opencode'] as const;\n\n/**\n * Generates the weather report from current outcome data.\n */\nexport function generateWeatherReport(\n  input: WeatherReportOptions,\n  config?: Partial<WeatherReportConfig>\n): WeatherReportResponse {\n  const cfg = { ...createDefaultWeatherConfig(), ...config };\n  const store = getOutcomeStore();\n  const includeAdaptive = input.includeAdaptive ?? true;\n\n  const summary = store.summarize(buildQuery(input.cli, input.category));\n\n  const cliWeather = buildCliWeather(summary, input);\n  const adaptiveBonuses = includeAdaptive ? computeAdaptiveBonuses(cfg) : [];\n  const tierRecommendations = buildTierRecommendations(summary);\n  const rateLimits = buildRateLimitReport();\n  const toolPerformance = buildToolPerformance();\n  const failureBreakdown = buildFailureBreakdown(input);\n  const agentHealth = buildAgentHealth();\n  const expertPerformance = buildExpertPerformance();\n  const base = {\n    overall: {\n      totalTasks: summary.totalTasks,\n      successRate: summary.successRate,\n      avgDurationMs: summary.avgDurationMs,\n    },\n    cliWeather,\n    adaptiveBonuses,\n    tierRecommendations,\n    ...(rateLimits.length > 0 ? { rateLimits } : {}),\n    ...(toolPerformance.length > 0 ? { toolPerformance } : {}),\n    ...(failureBreakdown.length > 0 ? { failureBreakdown } : {}),\n    ...(agentHealth !== undefined ? { agentHealth } : {}),\n    ...(expertPerformance.length > 0 ? { expertPerformance } : {}),\n    explorationRate: cfg.explorationRate,\n    coldStartThreshold: cfg.coldStartThreshold,\n    collectedAt: new Date().toISOString(),\n  };\n\n  if (includeAdaptive) {\n    return {\n      ...base,\n      learningInsights: buildLearningInsights(),\n      recommendedMappings: buildRecommendedMappings(),\n    };\n  }\n\n  return base;\n}\n\n/** Builds agent health from heartbeat monitor (Issue #1032). */\nfunction buildAgentHealth(): AgentHealthSummary | undefined {\n  const monitor = getHeartbeatMonitor();\n  if (monitor.activeCount === 0) return undefined;\n  const health = monitor.getHealth();\n  return {\n    activeSessions: health.activeSessions,\n    stalledSessions: health.stalledSessions,\n    sessions: health.sessions.map((s) => ({\n      sessionId: s.sessionId,\n      expertId: s.expertId,\n      health: s.health,\n      elapsedMs: s.elapsedMs,\n      timeSinceHeartbeatMs: s.timeSinceHeartbeatMs,\n      heartbeatCount: s.heartbeatCount,\n    })),\n  };\n}\n\n/** Builds rate limit report from tracked events (Issue #996). */\nfunction buildRateLimitReport(): readonly RateLimitReport[] {\n  return getRateLimitStats().map((s) => ({\n    provider: s.provider,\n    totalHits: s.totalHits,\n    lastHitAt: s.lastHitAt,\n    avgRetryAfterMs: s.avgRetryAfterMs,\n  }));\n}\n\n/**\n * Calculates adaptive specialization bonus for a given CLI+category.\n * Returns the adjustment on top of the static bonus.\n *\n * - Below cold-start threshold: returns 0 (no adjustment)\n * - Above threshold: scales bonus by observed success rate vs baseline\n * - Clamped to [-maxBonusAdjustment, +maxBonusAdjustment]\n */\nexport function getAdaptiveBonus(\n  cli: string,\n  category: TaskCategory,\n  config?: Partial<WeatherReportConfig>\n): number {\n  const cfg = { ...createDefaultWeatherConfig(), ...config };\n  const store = getOutcomeStore();\n  const cliName = cli as CliNameLiteral;\n\n  const outcomes = store.query({ cli: cliName, category });\n  if (outcomes.length < cfg.coldStartThreshold) return 0;\n\n  const thresholds = computeAdaptiveThresholds(store, cliName, category);\n  const successRate = outcomes.filter((o) => o.success).length / outcomes.length;\n  const delta = successRate - thresholds.baseline;\n\n  // Scale: +30% above baseline → +maxBonus (adaptive, not hardcoded)\n  const maxBonus = thresholds.maxBonus > 0 ? thresholds.maxBonus : cfg.maxBonusAdjustment;\n  const scaled = (delta / 0.3) * maxBonus;\n  return clamp(scaled, -maxBonus, maxBonus);\n}\n\n/**\n * Determines if exploration should override normal routing.\n * Uses epsilon-greedy: returns true with probability = explorationRate.\n */\nexport function shouldExplore(config?: Partial<WeatherReportConfig>): boolean {\n  const cfg = { ...createDefaultWeatherConfig(), ...config };\n  return Math.random() < cfg.explorationRate;\n}\n\n// ============================================================================\n// Internal Helpers\n// ============================================================================\n\nfunction buildQuery(\n  cli?: string,\n  category?: string\n): { cli?: CliNameLiteral; category?: TaskCategory } {\n  const query: { cli?: CliNameLiteral; category?: TaskCategory } = {};\n  if (cli !== undefined) query.cli = cli as CliNameLiteral;\n  if (category !== undefined) query.category = category as TaskCategory;\n  return query;\n}\n\nfunction buildCliWeather(\n  summary: PerformanceSummary,\n  input: WeatherReportOptions\n): readonly CliWeather[] {\n  const clis = input.cli !== undefined ? [input.cli] : [...CLI_NAMES];\n\n  return clis.map((cli) => {\n    const stats = summary.byCli.get(cli);\n    const store = getOutcomeStore();\n    const cliOutcomes = store.query({ cli: cli });\n\n    // Build per-category breakdown for this CLI\n    const byCategory = new Map<string, GroupStats>();\n    for (const cat of TASK_CATEGORIES) {\n      const catOutcomes = cliOutcomes.filter((o) => o.category === cat);\n      if (catOutcomes.length > 0) {\n        const sc = catOutcomes.filter((o) => o.success).length;\n        const td = catOutcomes.reduce((s, o) => s + o.durationMs, 0);\n        byCategory.set(cat, {\n          count: catOutcomes.length,\n          successRate: sc / catOutcomes.length,\n          avgDurationMs: td / catOutcomes.length,\n        });\n      }\n    }\n\n    return {\n      cli,\n      totalTasks: stats?.count ?? 0,\n      successRate: stats?.successRate ?? 0,\n      avgDurationMs: stats?.avgDurationMs ?? 0,\n      byCategory,\n    };\n  });\n}\n\nfunction computeAdaptiveBonuses(cfg: WeatherReportConfig): readonly AdaptiveBonus[] {\n  const bonuses: AdaptiveBonus[] = [];\n\n  for (const cli of CLI_NAMES) {\n    for (const category of TASK_CATEGORIES) {\n      const spec = getSpecialization(category);\n      const staticBonus = getStaticBonusForCli(cli, spec);\n      const store = getOutcomeStore();\n      const outcomes = store.query({ cli, category });\n      const sampleCount = outcomes.length;\n      const sufficient = sampleCount >= cfg.coldStartThreshold;\n      const adaptiveAdj = sufficient ? getAdaptiveBonus(cli, category, cfg) : 0;\n\n      // Only include entries with actual data or non-zero bonuses\n      if (sampleCount > 0 || staticBonus > 0 || adaptiveAdj !== 0) {\n        bonuses.push({\n          cli,\n          category,\n          staticBonus,\n          adaptiveBonus: Math.round(adaptiveAdj * 10) / 10,\n          sampleCount,\n          sufficient,\n        });\n      }\n    }\n  }\n\n  return bonuses;\n}\n\n/** Gets the static specialization bonus for a CLI in a given spec. */\nfunction getStaticBonusForCli(\n  cli: string,\n  spec: { primaryCli: string; secondaryCli: string; bonus: number }\n): number {\n  if (cli === spec.primaryCli) return spec.bonus;\n  if (cli === spec.secondaryCli) return Math.floor(spec.bonus / 2);\n  return 0;\n}\n\nfunction clamp(value: number, min: number, max: number): number {\n  return Math.min(max, Math.max(min, value));\n}\n\n/** Builds learning insights from adaptive thresholds (#901). */\nfunction buildLearningInsights(): readonly LearningInsight[] {\n  const store = getOutcomeStore();\n  const insights: LearningInsight[] = [];\n\n  for (const cli of CLI_NAMES) {\n    for (const category of TASK_CATEGORIES) {\n      const thresholds = computeAdaptiveThresholds(store, cli, category);\n      if (thresholds.sampleCount > 0) {\n        insights.push({\n          cli,\n          category,\n          trend: thresholds.trend,\n          confidence: thresholds.confidence,\n          adjustedBaseline: thresholds.baseline,\n          sampleCount: thresholds.sampleCount,\n        });\n      }\n    }\n  }\n\n  return insights;\n}\n\n/** Builds recommended CLI mappings per category for LinUCB cold-start (#952). */\nfunction buildRecommendedMappings(): readonly RecommendedMapping[] {\n  const store = getOutcomeStore();\n  const mappings: RecommendedMapping[] = [];\n\n  for (const category of TASK_CATEGORIES) {\n    let bestCli = '';\n    let bestRate = -1;\n    let bestCount = 0;\n\n    for (const cli of CLI_NAMES) {\n      const outcomes = store.query({ cli, category });\n      if (outcomes.length === 0) continue;\n      const rate = outcomes.filter((o) => o.success).length / outcomes.length;\n      if (rate > bestRate || (rate === bestRate && outcomes.length > bestCount)) {\n        bestCli = cli;\n        bestRate = rate;\n        bestCount = outcomes.length;\n      }\n    }\n\n    if (bestCli !== '') {\n      const confidence = bestCount >= 20 ? 'high' : bestCount >= 10 ? 'medium' : 'low';\n      mappings.push({\n        category,\n        recommendedCli: bestCli,\n        successRate: bestRate,\n        sampleCount: bestCount,\n        confidence: confidence,\n      });\n    }\n  }\n\n  return mappings;\n}\n\n/** Worker model prefix used by recordWorkerOutcomes (Issue #1323). */\nconst WORKER_MODEL_PREFIX = 'worker-';\n\n/** Finds the most common failure category among failed outcomes. */\nfunction findDominantError(\n  failed: ReadonlyArray<{ failureCategory?: string | undefined }>\n): string | undefined {\n  if (failed.length === 0) return undefined;\n  const counts = new Map<string, number>();\n  for (const f of failed) {\n    const cat = f.failureCategory ?? 'unknown';\n    counts.set(cat, (counts.get(cat) ?? 0) + 1);\n  }\n  let maxCount = 0;\n  let dominant: string | undefined;\n  for (const [cat, count] of counts) {\n    if (count > maxCount) {\n      maxCount = count;\n      dominant = cat;\n    }\n  }\n  return dominant;\n}\n\n/** Builds per-expert-role performance from worker dispatch outcomes (Issue #1324). */\nfunction buildExpertPerformance(): readonly ExpertPerformanceEntry[] {\n  const store = getOutcomeStore();\n  const allOutcomes = store.query();\n  const workerOutcomes = allOutcomes.filter((o) => o.model.startsWith(WORKER_MODEL_PREFIX));\n  if (workerOutcomes.length === 0) return [];\n\n  const byRole = new Map<string, typeof workerOutcomes>();\n  for (const o of workerOutcomes) {\n    const role = o.model.slice(WORKER_MODEL_PREFIX.length);\n    const existing = byRole.get(role) ?? [];\n    existing.push(o);\n    byRole.set(role, existing);\n  }\n\n  const entries: ExpertPerformanceEntry[] = [];\n  for (const [role, outcomes] of byRole) {\n    const successes = outcomes.filter((o) => o.success).length;\n    const totalDuration = outcomes.reduce((s, o) => s + o.durationMs, 0);\n    const dominantErrorPattern = findDominantError(outcomes.filter((o) => !o.success));\n\n    entries.push({\n      role,\n      totalTasks: outcomes.length,\n      successRate: successes / outcomes.length,\n      avgDurationMs: Math.round(totalDuration / outcomes.length),\n      ...(dominantErrorPattern !== undefined ? { dominantErrorPattern } : {}),\n    });\n  }\n\n  return entries.sort((a, b) => b.totalTasks - a.totalTasks);\n}\n\n/** Builds failure breakdown from failed outcomes (Issue #1025). */\nfunction buildFailureBreakdown(input: WeatherReportOptions): readonly FailureBreakdownEntry[] {\n  const store = getOutcomeStore();\n  const outcomes = store.query(buildQuery(input.cli, input.category));\n  const failed = outcomes.filter((o) => !o.success);\n  if (failed.length === 0) return [];\n\n  const counts = new Map<string, number>();\n  for (const o of failed) {\n    const cat = o.failureCategory ?? 'unknown';\n    counts.set(cat, (counts.get(cat) ?? 0) + 1);\n  }\n\n  const entries: FailureBreakdownEntry[] = [];\n  for (const [category, count] of counts) {\n    entries.push({\n      category,\n      count,\n      percentage: Math.round((count / failed.length) * 1000) / 10,\n    });\n  }\n  return entries.sort((a, b) => b.count - a.count);\n}\n\n/** Builds per-tool performance stats from recorded metrics (#1022). */\nfunction buildToolPerformance(): readonly ToolPerformanceEntry[] {\n  return getToolStats().map((s) => ({\n    toolName: s.toolName,\n    totalCalls: s.totalCalls,\n    successRate: Math.round(s.successRate * 1000) / 1000,\n    avgDurationMs: Math.round(s.avgDurationMs),\n    errorCount: s.errorCount,\n  }));\n}\n\n/** Generates tier recommendations from outcome summary (#895). */\nfunction buildTierRecommendations(summary: PerformanceSummary): readonly TierRecommendationEntry[] {\n  return generateTierRecommendations(summary).map((r) => ({\n    category: r.category,\n    direction: r.direction,\n    currentTier: r.currentTier,\n    recommendedTier: r.recommendedTier,\n    successRate: r.successRate,\n    sampleCount: r.sampleCount,\n    reason: r.reason,\n  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package/dist/chunk-UVQ7R4C4.js.map

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-{"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-data-dir.ts","../src/cli/doctor.ts","../src/cli/doctor-formatting.ts","../src/cli/setup-opencode.ts","../src/cli/setup-gemini.ts","../src/cli/setup-codex.ts","../src/cli/setup-wizard.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 .claude/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';\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/** 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: MCP Configuration\n  const { step: mcpStep, snippet, mcpResult } = runMcpConfigStep(env, parsedOptions);\n\n  // Step 3: Rules File\n  const { step: rulesStep, rulesPath } = runRulesStep(env, parsedOptions);\n\n  // Step 4: Hooks Configuration (Issue #416)\n  const { step: hooksStep, hookSnippet, hookResult } = runHooksStep(env, parsedOptions);\n\n  // Step 5: Data Directory Initialization (#1249)\n  const { step: dataDirStep, result: dataDirResult } = runDataDirStep(parsedOptions);\n\n  // Step 6: OpenCode MCP Configuration (#1253)\n  const openCodeStep = runOpenCodeStep(parsedOptions);\n\n  // Step 7: Gemini MCP Configuration (#1259)\n  const geminiStep = runGeminiStep(parsedOptions);\n\n  // Step 8: Codex MCP Configuration (#1263)\n  const codexStep = runCodexStep(parsedOptions);\n\n  const configStep = runConfigStep(projectRoot, parsedOptions); // Step 9\n  const steps = [\n    detectionStep,\n    mcpStep,\n    rulesStep,\n    hooksStep,\n    dataDirStep,\n    openCodeStep,\n    geminiStep,\n    codexStep,\n    configStep,\n  ];\n  steps.push(runValidationStep(steps)); // Step 10: 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}\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 * 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 * @returns Exit code (0 = success, 1 = failure)\n */\nexport async function setupCommandAsync(options: SetupCommandOptions = {}): Promise<number> {\n  // Run interactive wizard if requested\n  if (options.interactive === true) {\n    const wizardOptions = await runWizard();\n\n    if (wizardOptions === undefined) {\n      // User cancelled the wizard\n      return 1;\n    }\n\n    // Merge wizard options with any existing options (wizard options take precedence)\n    const mergedOptions = { ...options, ...wizardOptions };\n    delete (mergedOptions as SetupCommandOptions).interactive; // Remove interactive flag\n\n    const result = runSetup(mergedOptions);\n    printSetupResult(result, mergedOptions.verbose ?? false);\n    return result.success ? 0 : 1;\n  }\n\n  // Fall back to synchronous command\n  return setupCommand(options);\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      packageName = pkg['name'] as string | 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    hasClaudeRules: 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${VERSION}*\n`;\n}\n\n/**\n * Gets the rules file path.\n */\nexport function getRulesFilePath(projectRoot: string): string {\n  return join(projectRoot, '.claude', 'rules', 'nexus-agents.md');\n}\n\n/**\n * Creates the rules file.\n */\nexport function createRulesFile(projectRoot: string, dryRun: boolean): string {\n  const rulesPath = getRulesFilePath(projectRoot);\n  const content = generateRulesContent();\n\n  if (!dryRun) {\n    const rulesDir = dirname(rulesPath);\n    mkdirSync(rulesDir, { recursive: true });\n    writeFileSync(rulesPath, content, 'utf-8');\n  }\n\n  return rulesPath;\n}\n\n/**\n * Creates a backup of a file.\n */\nexport function backupFile(filePath: string): BackupInfo {\n  const content = readFileSync(filePath, 'utf-8');\n  const backupPath = `${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 * nexus-agents data directory initialization\n *\n * Pre-creates ~/.nexus-agents/ directory structure with proper permissions.\n * Used by `nexus-agents setup` to ensure data directories exist before first use.\n *\n * @module cli/setup-data-dir\n * (Source: Issue #1249 - Developer experience improvements)\n */\n\nimport { mkdirSync, existsSync } from 'node:fs';\nimport { homedir } from 'node:os';\nimport { join } from 'node:path';\nimport { DATA_SUBDIRECTORIES } from './doctor.js';\n\n/** Root data directory path. */\nexport const NEXUS_DATA_DIR = join(homedir(), '.nexus-agents');\n\n/** Subdirectories requiring restricted permissions (owner-only). */\nconst RESTRICTED_DIRS = new Set(['auth']);\n\n/**\n * Result of data directory initialization.\n */\nexport interface DataDirInitResult {\n  readonly success: boolean;\n  readonly rootPath: string;\n  readonly created: readonly string[];\n  readonly alreadyExisted: readonly string[];\n  readonly error: string | null;\n}\n\n/**\n * Creates the ~/.nexus-agents/ directory structure.\n * Sets restrictive permissions (0o700) on auth/ directory.\n *\n * @param dryRun - If true, reports what would be created without creating.\n * @returns Result of initialization.\n */\nexport function initDataDirectories(dryRun: boolean = false): DataDirInitResult {\n  const created: string[] = [];\n  const alreadyExisted: string[] = [];\n\n  try {\n    ensureDir(NEXUS_DATA_DIR, dryRun, created, alreadyExisted);\n\n    for (const subdir of DATA_SUBDIRECTORIES) {\n      const mode = RESTRICTED_DIRS.has(subdir) ? 0o700 : undefined;\n      ensureDir(join(NEXUS_DATA_DIR, subdir), dryRun, created, alreadyExisted, mode);\n    }\n\n    return { success: true, rootPath: NEXUS_DATA_DIR, created, alreadyExisted, error: null };\n  } catch (error: unknown) {\n    const msg = error instanceof Error ? error.message : String(error);\n    return { success: false, rootPath: NEXUS_DATA_DIR, created, alreadyExisted, error: msg };\n  }\n}\n\n/** Creates a single directory if it doesn't exist, tracking the result. */\nfunction ensureDir(\n  dirPath: string,\n  dryRun: boolean,\n  created: string[],\n  alreadyExisted: string[],\n  mode?: number\n): void {\n  if (existsSync(dirPath)) {\n    alreadyExisted.push(dirPath);\n    return;\n  }\n  if (!dryRun) {\n    mkdirSync(dirPath, { recursive: true, ...(mode !== undefined ? { mode } : {}) });\n  }\n  created.push(dirPath);\n}\n","/* eslint-disable max-lines -- Cohesive doctor command module (governance: 400-600 OK if cohesive) */\n/**\n * nexus-agents doctor command\n *\n * Health check utility for CLI integration validation.\n * Verifies CLI installations, versions, authentication, Node.js version,\n * API keys, configuration files, and MCP server readiness.\n *\n * (Source: Issue #91, cli-project_plan.md DevEx amendment)\n * (Source: Issue #422 - Doctor command validations)\n */\n\nimport { existsSync, readFileSync, accessSync, constants as fsConstants } from 'node:fs';\nimport { homedir } from 'node:os';\nimport { join } from 'node:path';\nimport { getTimeProvider, getErrorMessage } from '../core/index.js';\nimport {\n  isPersistenceEnabled,\n  LEARNING_DIR,\n  OUTCOMES_FILE,\n  RULES_FILE,\n} from '../config/learning-persistence.js';\nimport { createAllAdapters } from '../cli-adapters/factory.js';\nimport type { CliName, HealthStatus, CapacityStatus } from '../cli-adapters/types.js';\nimport { DEFAULT_MODEL_CAPABILITIES } from '../config/model-capabilities.js';\nimport { createServer } from '../mcp/server.js';\nimport { printDoctorResults } from './doctor-formatting.js';\n\n/** Required Node.js major version. */\nconst REQUIRED_NODE_MAJOR = 22;\n\n/** API key environment variable names. */\nconst API_KEY_VARS = ['ANTHROPIC_API_KEY', 'OPENAI_API_KEY', 'GOOGLE_AI_API_KEY'] as const;\n\n/** Configuration file paths to check (in order of priority). */\nconst CONFIG_FILE_PATHS = ['./nexus-agents.yaml', './nexus-agents.yml'] as const;\n\n/**\n * Check result for a single CLI.\n */\nexport interface CliCheckResult {\n  readonly name: CliName;\n  readonly installed: boolean;\n  readonly version: string;\n  readonly versionStatus: 'supported' | 'outdated' | 'unsupported' | 'breaking';\n  readonly authenticated: boolean;\n  readonly authMethod?: string;\n  readonly capacity?: CapacityStatus;\n  readonly error?: string;\n  readonly fix?: string;\n}\n\n/**\n * Node.js version check result.\n */\nexport interface NodeVersionCheck {\n  readonly version: string;\n  readonly major: number;\n  readonly supported: boolean;\n}\n\n/**\n * API key check result.\n */\nexport interface ApiKeyCheck {\n  readonly name: string;\n  readonly configured: boolean;\n}\n\n/**\n * Configuration file check result.\n */\nexport interface ConfigFileCheck {\n  readonly found: boolean;\n  readonly path: string | null;\n}\n\n/**\n * Model availability advisory entry (#890).\n */\nexport interface ModelAdvisory {\n  readonly modelId: string;\n  readonly displayName: string;\n  readonly cliName: string;\n  readonly available: boolean;\n  readonly reason: string;\n}\n\n/**\n * Learning persistence health check result (#1017).\n */\nexport interface LearningPersistenceCheck {\n  readonly enabled: boolean;\n  readonly dirExists: boolean;\n  readonly dirWritable: boolean;\n  readonly outcomeCount: number;\n  readonly ruleCount: number;\n  readonly rulesLastSaved: string | null;\n  readonly error: string | null;\n}\n\n/**\n * Registry advisory summary (#890).\n */\nexport interface RegistryAdvisory {\n  readonly totalModels: number;\n  readonly availableModels: number;\n  readonly unavailableModels: number;\n  readonly models: readonly ModelAdvisory[];\n}\n\n/**\n * SQLite (better-sqlite3) availability check (#1249).\n */\nexport interface SqliteCheck {\n  readonly available: boolean;\n  readonly error: string | null;\n}\n\n/**\n * Data directory health check (#1249).\n * Reports status of ~/.nexus-agents/ and its subdirectories.\n */\nexport interface DataDirectoryCheck {\n  readonly rootExists: boolean;\n  readonly rootPath: string;\n  readonly subdirectories: readonly DataSubdirStatus[];\n}\n\n/**\n * Status of a single data subdirectory.\n */\nexport interface DataSubdirStatus {\n  readonly name: string;\n  readonly path: string;\n  readonly exists: boolean;\n}\n\n/** Standard data subdirectories under ~/.nexus-agents/. */\nexport const DATA_SUBDIRECTORIES = [\n  'memory',\n  'memory/beliefs',\n  'learning',\n  'sessions',\n  'audit',\n  'voting',\n  'auth',\n  'research',\n  'checkpoints',\n] as const;\n\n/**\n * Complete doctor check results.\n */\nexport interface DoctorResult {\n  readonly clis: CliCheckResult[];\n  readonly nodeVersion: NodeVersionCheck;\n  readonly apiKeys: ApiKeyCheck[];\n  readonly configFile: ConfigFileCheck;\n  readonly mcpServerReady: boolean;\n  readonly mcpClientReady: boolean;\n  /** Model registry advisory — which models are available (#890). */\n  readonly registryAdvisory: RegistryAdvisory;\n  /** Learning persistence health check (#1017). */\n  readonly learningPersistence: LearningPersistenceCheck;\n  /** SQLite (better-sqlite3) availability (#1249). */\n  readonly sqliteCheck: SqliteCheck;\n  /** Data directory health (#1249). */\n  readonly dataDirectory: DataDirectoryCheck;\n  readonly allHealthy: boolean;\n  readonly timestamp: Date;\n}\n\n/**\n * Gets the CLI install/upgrade fix command.\n */\nfunction getFixCommand(name: CliName, issue: 'install' | 'upgrade' | 'auth'): string {\n  const commands: Record<CliName, Record<string, string>> = {\n    claude: {\n      install: 'npm install -g @anthropic-ai/claude-code',\n      upgrade: 'npm update -g @anthropic-ai/claude-code',\n      auth: 'claude auth login',\n    },\n    gemini: {\n      install: 'npm install -g @google/gemini-cli',\n      upgrade: 'npm update -g @google/gemini-cli',\n      auth: 'gemini auth login',\n    },\n    codex: {\n      install: 'npm install -g @openai/codex',\n      upgrade: 'npm update -g @openai/codex',\n      auth: 'codex auth login',\n    },\n    opencode: {\n      install: 'npm install -g opencode-ai',\n      upgrade: 'npm update -g opencode-ai',\n      auth: 'opencode auth login',\n    },\n  };\n  return commands[name][issue] ?? '';\n}\n\n/**\n * Creates a result for when a CLI is not found.\n */\nfunction createNotFoundResult(name: CliName, errorMsg: string): CliCheckResult {\n  return {\n    name,\n    installed: false,\n    version: 'N/A',\n    versionStatus: 'unsupported',\n    authenticated: false,\n    error: errorMsg,\n    fix: getFixCommand(name, 'install'),\n  };\n}\n\n/**\n * Determines the authentication method based on CLI name.\n * CLIs use their own auth mechanisms - we report the method type\n * rather than assuming a specific one like 'OAuth'.\n */\nfunction detectAuthMethod(name: CliName): string {\n  const authMethods: Record<CliName, string> = {\n    claude: 'CLI auth',\n    gemini: 'ADC/CLI auth',\n    codex: 'CLI auth',\n    opencode: 'CLI auth',\n  };\n  return authMethods[name];\n}\n\n/**\n * Creates a result from a successful health check.\n */\nfunction createHealthyResult(\n  name: CliName,\n  health: HealthStatus,\n  capacity?: CapacityStatus\n): CliCheckResult {\n  const authenticated = health.healthy;\n\n  const result: CliCheckResult = {\n    name,\n    installed: true,\n    version: health.version,\n    versionStatus: health.versionStatus,\n    authenticated,\n    ...(authenticated && { authMethod: detectAuthMethod(name) }),\n    ...(capacity !== undefined && { capacity }),\n  };\n\n  if (health.message !== undefined && health.message !== '') {\n    return { ...result, error: health.message };\n  }\n  if (!authenticated) {\n    return { ...result, fix: getFixCommand(name, 'auth') };\n  }\n  if (health.versionStatus === 'outdated') {\n    return { ...result, fix: getFixCommand(name, 'upgrade') };\n  }\n\n  return result;\n}\n\n/**\n * Runs health check on a single CLI adapter.\n */\nasync function checkCli(name: CliName): Promise<CliCheckResult> {\n  const adapters = createAllAdapters();\n  const adapter = adapters.get(name);\n\n  if (!adapter) {\n    return createNotFoundResult(name, 'Adapter not available');\n  }\n\n  try {\n    const health: HealthStatus = await adapter.healthCheck();\n    let capacity: CapacityStatus | undefined;\n\n    try {\n      capacity = await adapter.getCapacity();\n    } catch (capErr: unknown) {\n      // Capacity check is optional — some adapters don't support it\n      void capErr; // Logged at debug via adapter internals\n    }\n\n    return createHealthyResult(name, health, capacity);\n  } catch (error) {\n    const message = getErrorMessage(error);\n    const isNotFound = message.includes('ENOENT') || message.includes('not found');\n    return createNotFoundResult(name, isNotFound ? 'Not found in PATH' : message);\n  }\n}\n\n/**\n * Checks the Node.js version against the required version.\n */\nfunction checkNodeVersion(): NodeVersionCheck {\n  const version = process.version;\n  const major = Number(version.slice(1).split('.')[0]);\n  return {\n    version,\n    major,\n    supported: major >= REQUIRED_NODE_MAJOR,\n  };\n}\n\n/**\n * Checks which API keys are configured in the environment.\n * Does NOT expose the actual key values - only reports presence.\n */\nfunction checkApiKeys(): ApiKeyCheck[] {\n  return API_KEY_VARS.map((name) => ({\n    name,\n    configured: typeof process.env[name] === 'string' && process.env[name] !== '',\n  }));\n}\n\n/**\n * Checks for the existence of a configuration file.\n */\nfunction checkConfigFile(): ConfigFileCheck {\n  for (const configPath of CONFIG_FILE_PATHS) {\n    if (existsSync(configPath)) {\n      return { found: true, path: configPath };\n    }\n  }\n  return { found: false, path: null };\n}\n\n/**\n * Validates that the MCP server can be created successfully.\n * This is a lightweight check that verifies server instantiation works.\n */\nfunction checkMcpServerReady(): boolean {\n  try {\n    const result = createServer({ name: 'nexus-agents-doctor-check' });\n    return result.ok;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Builds model registry advisory based on detected CLI availability (#890).\n */\nfunction buildRegistryAdvisory(cliResults: CliCheckResult[]): RegistryAdvisory {\n  const installedClis = new Set(cliResults.filter((c) => c.installed).map((c) => c.name));\n\n  const models: ModelAdvisory[] = DEFAULT_MODEL_CAPABILITIES.models\n    .filter((m) => m.cliName !== undefined)\n    .map((m) => {\n      const cliName = m.cliName as string;\n      const available = installedClis.has(cliName as CliName);\n      const reason = available ? `${cliName} CLI is installed` : `${cliName} CLI is not installed`;\n      return { modelId: m.id, displayName: m.displayName, cliName, available, reason };\n    });\n\n  return {\n    totalModels: models.length,\n    availableModels: models.filter((m) => m.available).length,\n    unavailableModels: models.filter((m) => !m.available).length,\n    models,\n  };\n}\n\n/** Counts non-empty lines in a JSONL file. Returns 0 if file doesn't exist. */\nfunction countJsonlLines(filePath: string): number {\n  if (!existsSync(filePath)) return 0;\n  return readFileSync(filePath, 'utf-8')\n    .split('\\n')\n    .filter((l) => l.trim().length > 0).length;\n}\n\n/** Reads rules snapshot metadata. Returns count and savedAt. */\nfunction readRulesMetadata(filePath: string): { count: number; savedAt: string | null } {\n  if (!existsSync(filePath)) return { count: 0, savedAt: null };\n  try {\n    const raw = JSON.parse(readFileSync(filePath, 'utf-8')) as Record<string, unknown>;\n    const rules = raw['rules'];\n    const saved = raw['savedAt'];\n    return {\n      count: Array.isArray(rules) ? rules.length : 0,\n      savedAt: typeof saved === 'string' ? saved : null,\n    };\n  } catch {\n    return { count: 0, savedAt: null };\n  }\n}\n\n/** Checks if a directory exists and is writable. */\nfunction checkDirAccess(dir: string): { exists: boolean; writable: boolean } {\n  const exists = existsSync(dir);\n  if (!exists) return { exists: false, writable: false };\n  try {\n    accessSync(dir, fsConstants.W_OK);\n    return { exists: true, writable: true };\n  } catch {\n    return { exists: true, writable: false };\n  }\n}\n\nconst DISABLED_CHECK: LearningPersistenceCheck = {\n  enabled: false,\n  dirExists: false,\n  dirWritable: false,\n  outcomeCount: 0,\n  ruleCount: 0,\n  rulesLastSaved: null,\n  error: null,\n};\n\n/** Checks learning persistence health (#1017). */\nfunction checkLearningPersistence(): LearningPersistenceCheck {\n  if (!isPersistenceEnabled()) return DISABLED_CHECK;\n  try {\n    const { exists: dirExists, writable: dirWritable } = checkDirAccess(LEARNING_DIR);\n    const outcomeCount = countJsonlLines(OUTCOMES_FILE);\n    const { count: ruleCount, savedAt: rulesLastSaved } = readRulesMetadata(RULES_FILE);\n    return {\n      enabled: true,\n      dirExists,\n      dirWritable,\n      outcomeCount,\n      ruleCount,\n      rulesLastSaved,\n      error: null,\n    };\n  } catch (error: unknown) {\n    return {\n      enabled: true,\n      dirExists: false,\n      dirWritable: false,\n      outcomeCount: 0,\n      ruleCount: 0,\n      rulesLastSaved: null,\n      error: getErrorMessage(error),\n    };\n  }\n}\n\n/**\n * Checks if better-sqlite3 is available (#1249).\n * Memory backends (agentic, adaptive, typed, mobimem, decay) require it.\n */\nasync function checkSqlite(): Promise<SqliteCheck> {\n  try {\n    await import('better-sqlite3');\n    return { available: true, error: null };\n  } catch (error: unknown) {\n    const msg = getErrorMessage(error);\n    const isNotFound = msg.includes('Cannot find') || msg.includes('MODULE_NOT_FOUND');\n    return {\n      available: false,\n      error: isNotFound\n        ? 'better-sqlite3 not installed — 5 memory backends unavailable'\n        : `better-sqlite3 load error: ${msg}`,\n    };\n  }\n}\n\n/**\n * Checks the ~/.nexus-agents/ data directory health (#1249).\n */\nfunction checkDataDirectory(): DataDirectoryCheck {\n  const rootPath = join(homedir(), '.nexus-agents');\n  const rootExists = existsSync(rootPath);\n\n  const subdirectories: DataSubdirStatus[] = DATA_SUBDIRECTORIES.map((name) => {\n    const fullPath = join(rootPath, name);\n    return { name, path: fullPath, exists: existsSync(fullPath) };\n  });\n\n  return { rootExists, rootPath, subdirectories };\n}\n\n/**\n * Runs the complete doctor check.\n */\nexport async function runDoctor(): Promise<DoctorResult> {\n  const clis = await Promise.all([\n    checkCli('claude'),\n    checkCli('gemini'),\n    checkCli('codex'),\n    checkCli('opencode'),\n  ]);\n  const nodeVersion = checkNodeVersion();\n  const apiKeys = checkApiKeys();\n  const configFile = checkConfigFile();\n  const mcpServerReady = checkMcpServerReady();\n  const codexCheck = clis.find((c) => c.name === 'codex');\n  const mcpClientReady = codexCheck?.installed ?? false;\n  const registryAdvisory = buildRegistryAdvisory(clis);\n  const learningPersistence = checkLearningPersistence();\n  const sqliteCheck = await checkSqlite();\n  const dataDirectory = checkDataDirectory();\n\n  // At least one API key configured or one CLI authenticated\n  const hasAuthMethod =\n    apiKeys.some((k) => k.configured) || clis.some((c) => c.installed && c.authenticated);\n\n  const allHealthy =\n    nodeVersion.supported &&\n    hasAuthMethod &&\n    mcpServerReady &&\n    clis.every((c) => c.installed && c.authenticated && c.versionStatus !== 'unsupported');\n\n  return {\n    clis,\n    nodeVersion,\n    apiKeys,\n    configFile,\n    mcpServerReady,\n    mcpClientReady,\n    registryAdvisory,\n    learningPersistence,\n    sqliteCheck,\n    dataDirectory,\n    allHealthy,\n    timestamp: new Date(getTimeProvider().now()),\n  };\n}\n\n/** Doctor command options. */\nexport interface DoctorOptions {\n  /** Auto-fix safe issues (run setup, generate config). */\n  readonly fix?: boolean;\n}\n\n/**\n * Runs the doctor command and prints results.\n * Returns exit code (0 = healthy, 1 = issues found).\n */\nexport async function doctorCommand(options: DoctorOptions = {}): Promise<number> {\n  const result = await runDoctor();\n  printDoctorResults(result);\n\n  if (options.fix === true) {\n    await runDoctorFix(result);\n  }\n\n  return result.allHealthy ? 0 : 1;\n}\n\n/**\n * Auto-fixes safe issues found by doctor (#1254).\n * Only runs our own code — never execs external package managers.\n */\nasync function runDoctorFix(result: DoctorResult): Promise<void> {\n  const writeLine = (text: string): void => {\n    process.stdout.write(text + '\\n');\n  };\n\n  writeLine('');\n  writeLine('\\x1b[1mAuto-fix\\x1b[0m');\n  writeLine('─'.repeat(40));\n\n  let fixCount = 0;\n\n  // Fix: data directories\n  if (\n    !result.dataDirectory.rootExists ||\n    result.dataDirectory.subdirectories.some((d) => !d.exists)\n  ) {\n    const { runSetup } = await import('./setup-command.js');\n    const setupResult = runSetup({\n      skipMcp: true,\n      skipRules: true,\n      skipHooks: true,\n      skipConfig: true,\n      skipOpencode: true,\n    });\n    if (setupResult.success) {\n      writeLine('✓ Created missing data directories');\n      fixCount++;\n    }\n  }\n\n  // Fix: config file\n  if (!result.configFile.found) {\n    const { runConfigInitSync } = await import('./setup-config.js');\n    const configResult = runConfigInitSync(process.cwd(), false, false);\n    if (configResult.success && configResult.created) {\n      writeLine(`✓ Generated config: ${configResult.path}`);\n      fixCount++;\n    }\n  }\n\n  // Display-only: better-sqlite3\n  if (!result.sqliteCheck.available) {\n    writeLine('');\n    writeLine('⚠ better-sqlite3 not installed (manual step required):');\n    writeLine('  npm install -g better-sqlite3');\n  }\n\n  if (fixCount > 0) {\n    writeLine('');\n    writeLine(\n      `\\x1b[32m${String(fixCount)} issue(s) fixed.\\x1b[0m Re-run \\x1b[1mnexus-agents doctor\\x1b[0m to verify.`\n    );\n  } else {\n    writeLine('No auto-fixable issues found.');\n  }\n  writeLine('');\n}\n\n// Re-export printDoctorResults for backward compatibility\nexport { printDoctorResults } from './doctor-formatting.js';\n","/**\n * nexus-agents doctor command - Formatting utilities\n *\n * Terminal output formatting for doctor command results.\n * Extracted to comply with 400-line file limit.\n *\n * (Source: Issue #422 - Doctor command validations)\n */\n\nimport { DEFAULT_CAPABILITIES } from '../cli-adapters/types.js';\nimport type { CapacityStatus } from '../cli-adapters/types.js';\nimport type {\n  CliCheckResult,\n  NodeVersionCheck,\n  ApiKeyCheck,\n  ConfigFileCheck,\n  RegistryAdvisory,\n  LearningPersistenceCheck,\n  SqliteCheck,\n  DataDirectoryCheck,\n  DoctorResult,\n} from './doctor.js';\nimport { colors, symbols, writeLine } from './ansi-output.js';\nimport { capitalize } from '../utils/text-utils.js';\n\n/** Required Node.js major version (for warning message). */\nconst REQUIRED_NODE_MAJOR = 22;\n\n/**\n * Formats a status symbol with color.\n */\nfunction formatStatus(healthy: boolean, warn = false): string {\n  if (healthy) return `${colors.green}${symbols.check}${colors.reset}`;\n  if (warn) return `${colors.yellow}${symbols.warn}${colors.reset}`;\n  return `${colors.red}${symbols.cross}${colors.reset}`;\n}\n\n/**\n * Formats version status with color.\n */\nfunction formatVersionStatus(status: string): string {\n  switch (status) {\n    case 'supported':\n      return `${colors.green}supported${colors.reset}`;\n    case 'outdated':\n      return `${colors.yellow}outdated${colors.reset}`;\n    case 'unsupported':\n    case 'breaking':\n      return `${colors.red}${status}${colors.reset}`;\n    default:\n      return status;\n  }\n}\n\n/**\n * Formats capacity as percentage string.\n */\nfunction formatCapacity(capacity?: CapacityStatus): string {\n  if (capacity === undefined) return 'Unknown';\n  const remaining = 100 - capacity.utilizationPercent;\n  const remainingStr = String(remaining);\n  if (remaining > 80) return `${colors.green}${remainingStr}% remaining${colors.reset}`;\n  if (remaining > 20) return `${colors.yellow}${remainingStr}% remaining${colors.reset}`;\n  return `${colors.red}${remainingStr}% remaining${colors.reset}`;\n}\n\n/**\n * Prints details for an installed CLI.\n */\nfunction printInstalledCliDetails(cli: CliCheckResult): void {\n  writeLine(`  Version: ${cli.version} (${formatVersionStatus(cli.versionStatus)})`);\n\n  const authText = cli.authenticated\n    ? `${colors.green}${cli.authMethod ?? 'Authenticated'}${colors.reset}`\n    : `${colors.red}Not authenticated${colors.reset}`;\n  writeLine(`  Auth: ${authText}`);\n\n  if (cli.capacity !== undefined) {\n    writeLine(`  Capacity: ${formatCapacity(cli.capacity)}`);\n  }\n}\n\n/**\n * Prints a single CLI result.\n */\nfunction printCliResult(cli: CliCheckResult): void {\n  const status = cli.installed && cli.authenticated;\n  const warn = cli.installed && (!cli.authenticated || cli.versionStatus === 'outdated');\n\n  writeLine(\n    `${formatStatus(status, warn)} ${colors.bold}${capitalize(cli.name)} CLI${colors.reset}`\n  );\n\n  if (cli.installed) {\n    printInstalledCliDetails(cli);\n  } else {\n    const errorText = cli.error ?? 'Not installed';\n    writeLine(`  ${colors.red}Error: ${errorText}${colors.reset}`);\n  }\n\n  if (cli.fix !== undefined && cli.fix !== '') {\n    writeLine(`  ${colors.dim}Fix: ${cli.fix}${colors.reset}`);\n  }\n\n  writeLine('');\n}\n\n/**\n * Prints capability summary for installed CLIs.\n */\nfunction printCapabilities(clis: CliCheckResult[]): void {\n  const installedClis = clis.filter((c) => c.installed);\n\n  if (installedClis.length === 0) {\n    writeLine(`${formatStatus(false)} No CLIs installed`);\n    return;\n  }\n\n  const caps = DEFAULT_CAPABILITIES;\n  const bestReasoning = installedClis.reduce((best, c) =>\n    caps[c.name].reasoning > caps[best.name].reasoning ? c : best\n  );\n  const bestContext = installedClis.reduce((best, c) =>\n    caps[c.name].contextWindow > caps[best.name].contextWindow ? c : best\n  );\n  const bestSpeed = installedClis.reduce((best, c) =>\n    caps[c.name].speed > caps[best.name].speed ? c : best\n  );\n\n  const contextTokensK = (caps[bestContext.name].contextWindow / 1000).toFixed(0);\n\n  writeLine(\n    `${formatStatus(true)} Complex reasoning: ${colors.bold}${capitalize(bestReasoning.name)}${colors.reset}`\n  );\n  writeLine(\n    `${formatStatus(true)} Large context: ${colors.bold}${capitalize(bestContext.name)}${colors.reset} (${contextTokensK}K tokens)`\n  );\n  writeLine(\n    `${formatStatus(true)} Fast execution: ${colors.bold}${capitalize(bestSpeed.name)}${colors.reset}`\n  );\n}\n\n/**\n * Prints Node.js version check result.\n */\nfunction printNodeVersionCheck(check: NodeVersionCheck): void {\n  const versionText = check.supported\n    ? `${colors.green}${check.version}${colors.reset}`\n    : `${colors.yellow}${check.version}${colors.reset}`;\n  writeLine(`${formatStatus(check.supported, !check.supported)} Node.js version: ${versionText}`);\n  if (!check.supported) {\n    writeLine(\n      `  ${colors.dim}Warning: Node.js ${String(REQUIRED_NODE_MAJOR)}.x LTS required${colors.reset}`\n    );\n  }\n}\n\n/**\n * Prints API key configuration check results.\n */\nfunction printApiKeysCheck(keys: ApiKeyCheck[]): void {\n  const configuredCount = keys.filter((k) => k.configured).length;\n  const configuredNames = keys.filter((k) => k.configured).map((k) => k.name);\n  const hasAny = configuredCount > 0;\n\n  writeLine(\n    `${formatStatus(hasAny, !hasAny)} API keys configured: ${String(configuredCount)} of ${String(keys.length)}`\n  );\n  if (hasAny) {\n    writeLine(`  ${colors.dim}Keys: ${configuredNames.join(', ')}${colors.reset}`);\n  } else {\n    writeLine(\n      `  ${colors.dim}Set ANTHROPIC_API_KEY, OPENAI_API_KEY, or GOOGLE_AI_API_KEY${colors.reset}`\n    );\n  }\n}\n\n/**\n * Prints configuration file check result.\n */\nfunction printConfigFileCheck(check: ConfigFileCheck): void {\n  if (check.found && check.path !== null) {\n    writeLine(`${formatStatus(true)} Configuration loaded: ${check.path}`);\n  } else {\n    writeLine(`${formatStatus(false, true)} Configuration file: Not found`);\n    writeLine(`  ${colors.dim}Run: nexus-agents config init${colors.reset}`);\n  }\n}\n\n/**\n * Prints model registry advisory (#890).\n */\nfunction printRegistryAdvisory(advisory: RegistryAdvisory): void {\n  const allAvailable = advisory.unavailableModels === 0;\n  const countText = `${String(advisory.availableModels)} of ${String(advisory.totalModels)}`;\n  writeLine(`${formatStatus(allAvailable, !allAvailable)} Models available: ${countText}`);\n  if (advisory.unavailableModels > 0) {\n    const missing = advisory.models.filter((m) => !m.available);\n    for (const m of missing) {\n      writeLine(`  ${colors.dim}${m.displayName} — ${m.reason}${colors.reset}`);\n    }\n  }\n}\n\n/**\n * Prints learning persistence health check (#1017).\n */\nfunction printLearningPersistence(check: LearningPersistenceCheck): void {\n  if (!check.enabled) {\n    writeLine(`${formatStatus(true)} Learning persistence: ${colors.dim}Disabled${colors.reset}`);\n    writeLine(`  ${colors.dim}Set NEXUS_PERSIST_LEARNING=true to enable${colors.reset}`);\n    return;\n  }\n\n  const healthy = check.dirExists && check.dirWritable && check.error === null;\n  writeLine(`${formatStatus(healthy, !healthy)} Learning persistence: Enabled`);\n\n  if (check.error !== null) {\n    writeLine(`  ${colors.red}Error: ${check.error}${colors.reset}`);\n    return;\n  }\n\n  const dirStatus = check.dirExists\n    ? check.dirWritable\n      ? `${colors.green}writable${colors.reset}`\n      : `${colors.red}not writable${colors.reset}`\n    : `${colors.yellow}not created yet${colors.reset}`;\n  writeLine(`  Data directory: ${dirStatus}`);\n  writeLine(`  Outcomes: ${String(check.outcomeCount)} recorded`);\n  writeLine(`  Distilled rules: ${String(check.ruleCount)} active`);\n  if (check.rulesLastSaved !== null) {\n    writeLine(`  Rules last saved: ${check.rulesLastSaved}`);\n  }\n}\n\n/**\n * Prints SQLite (better-sqlite3) availability check (#1249).\n */\nfunction printSqliteCheck(check: SqliteCheck): void {\n  if (check.available) {\n    writeLine(\n      `${formatStatus(true)} SQLite (better-sqlite3): ${colors.green}Available${colors.reset}`\n    );\n  } else {\n    writeLine(\n      `${formatStatus(false, true)} SQLite (better-sqlite3): ${colors.yellow}Not available${colors.reset}`\n    );\n    writeLine(\n      `  ${colors.dim}Memory backends (agentic, adaptive, typed) require it${colors.reset}`\n    );\n    writeLine(`  ${colors.dim}Fix: npm install -g better-sqlite3${colors.reset}`);\n  }\n}\n\n/**\n * Prints data directory health check (#1249).\n */\nfunction printDataDirectory(check: DataDirectoryCheck): void {\n  if (check.rootExists) {\n    const existCount = check.subdirectories.filter((d) => d.exists).length;\n    const totalCount = check.subdirectories.length;\n    const allExist = existCount === totalCount;\n    writeLine(\n      `${formatStatus(allExist, !allExist)} Data directory: ${check.rootPath} (${String(existCount)}/${String(totalCount)} subdirs)`\n    );\n    if (!allExist) {\n      const missing = check.subdirectories.filter((d) => !d.exists);\n      for (const dir of missing) {\n        writeLine(`  ${colors.dim}Missing: ${dir.name}/${colors.reset}`);\n      }\n      writeLine(`  ${colors.dim}Fix: nexus-agents setup${colors.reset}`);\n    }\n  } else {\n    writeLine(\n      `${formatStatus(false, true)} Data directory: ${colors.yellow}Not created${colors.reset}`\n    );\n    writeLine(`  ${colors.dim}Run: nexus-agents setup${colors.reset}`);\n  }\n}\n\n/** Prints the summary line with issue count. */\nfunction printDoctorSummary(result: DoctorResult): void {\n  const unhealthyCount = result.clis.filter((c) => !c.installed || !c.authenticated).length;\n  const nodeIssue = result.nodeVersion.supported ? 0 : 1;\n  const totalIssues = unhealthyCount + nodeIssue + (result.mcpServerReady ? 0 : 1);\n  const summary = result.allHealthy\n    ? `${colors.green}${colors.bold}Status: Ready${colors.reset}`\n    : `${colors.yellow}${colors.bold}Summary: ${String(totalIssues)} issue(s) found${colors.reset}`;\n  writeLine(summary);\n  writeLine('');\n}\n\n/**\n * Prints the doctor results to stdout.\n */\nexport function printDoctorResults(result: DoctorResult): void {\n  writeLine('');\n  writeLine(`${colors.bold}Nexus Agents Doctor${colors.reset}`);\n  writeLine('===================');\n  writeLine('');\n\n  writeLine(`${colors.cyan}Checking environment...${colors.reset}`);\n  writeLine('');\n  printNodeVersionCheck(result.nodeVersion);\n  printApiKeysCheck(result.apiKeys);\n  printConfigFileCheck(result.configFile);\n  writeLine('');\n\n  writeLine(`${colors.cyan}Checking CLI installations...${colors.reset}`);\n  writeLine('');\n  for (const cli of result.clis) {\n    printCliResult(cli);\n  }\n\n  writeLine(`${colors.cyan}Checking MCP configuration...${colors.reset}`);\n  writeLine('');\n  writeLine(\n    `${formatStatus(result.mcpServerReady)} MCP Server mode: ${result.mcpServerReady ? 'Ready' : 'Not ready'}`\n  );\n  writeLine(\n    `${formatStatus(result.mcpClientReady)} MCP Client mode: ${result.mcpClientReady ? 'Ready (Codex mcp-server)' : 'Not ready (Codex not installed)'}`\n  );\n  writeLine('');\n\n  writeLine(`${colors.cyan}Checking capabilities...${colors.reset}`);\n  writeLine('');\n  printCapabilities(result.clis);\n  writeLine('');\n\n  writeLine(`${colors.cyan}Checking model registry...${colors.reset}`);\n  writeLine('');\n  printRegistryAdvisory(result.registryAdvisory);\n  writeLine('');\n\n  writeLine(`${colors.cyan}Checking learning subsystem...${colors.reset}`);\n  writeLine('');\n  printLearningPersistence(result.learningPersistence);\n  writeLine('');\n\n  writeLine(`${colors.cyan}Checking data storage...${colors.reset}`);\n  writeLine('');\n  printSqliteCheck(result.sqliteCheck);\n  printDataDirectory(result.dataDirectory);\n  writeLine('');\n\n  printDoctorSummary(result);\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 (.claude/rules/nexus-agents.md)');\n    writeLine('  - Hooks for session tracking');\n  } else {\n    writeLine('Will configure:');\n    writeLine('  - Rules file (.claude/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 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