nexus-agents 2.71.0 → 2.72.1

package/dist/chunk-5MHIWRKB.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/adapters/base-adapter.ts","../src/adapters/streaming-types.ts","../src/adapters/stream-operators-helpers.ts","../src/adapters/stream-operators.ts","../src/adapters/streaming.ts"],"sourcesContent":["/**\n * nexus-agents/adapters - Base Adapter\n *\n * Abstract base class that all model adapters extend.\n * Provides common functionality for token counting, logging, error transformation,\n * and capability checking.\n */\n\nimport type {\n  Result,\n  IModelAdapter,\n  CompletionRequest,\n  CompletionResponse,\n  StreamChunk,\n  ILogger,\n  ModelCapability,\n} from '../core/index.js';\nimport { getErrorMessage } from '../core/index.js';\nimport { isRateLimitLikeError } from './rate-limit-detector.js';\n\nimport {\n  ok,\n  err,\n  ConfigError,\n  ModelError,\n  ErrorCode,\n  createLogger,\n  getTokenEstimator,\n  type NexusErrorOptions,\n} from '../core/index.js';\n\n/**\n * Configuration options for BaseAdapter.\n */\nexport interface BaseAdapterConfig {\n  /** Provider identifier (e.g., 'anthropic', 'openai') */\n  providerId: string;\n  /** Model identifier (e.g., 'claude-sonnet-4', 'gpt-4o') */\n  modelId: string;\n  /** Capabilities this model supports */\n  capabilities: readonly ModelCapability[];\n  /** Optional custom logger */\n  logger?: ILogger;\n  /** API key for authentication (optional, may come from environment) */\n  apiKey?: string;\n  /** Base URL for the API (optional, uses provider default) */\n  baseUrl?: string;\n  /** Request timeout in milliseconds */\n  timeout?: number;\n  /** Maximum number of retries for failed requests */\n  maxRetries?: number;\n}\n\n/**\n * Extended ModelError that supports specific error codes.\n *\n * While ModelError from core uses MODEL_ERROR by default, this subclass\n * allows adapters to specify more granular error codes like\n * MODEL_RATE_LIMITED, MODEL_TIMEOUT, etc.\n *\n * Extends ModelError so `instanceof ModelError` checks pass naturally\n * without requiring `as unknown as ModelError` casts.\n */\nexport class AdapterModelError extends ModelError {\n  constructor(message: string, options: NexusErrorOptions) {\n    super(message, options);\n    this.name = 'ModelError';\n  }\n}\n\n// ============================================================================\n// API Key Validation Helpers (#1446 — DRY extraction)\n// ============================================================================\n\n/**\n * Returns true if the given API key is missing or blank.\n */\nexport function isApiKeyMissing(apiKey: string | undefined): boolean {\n  return apiKey === undefined || apiKey === '' || apiKey.trim() === '';\n}\n\n/**\n * Validates API key presence in constructor — throws ConfigError if missing.\n * Use in adapter constructors where throwing is appropriate.\n */\nexport function requireApiKey(\n  apiKey: string | undefined,\n  providerName: string,\n  modelId: string\n): void {\n  if (isApiKeyMissing(apiKey)) {\n    throw new ConfigError(`${providerName} API key is required`, {\n      context: { providerId: providerName.toLowerCase(), modelId },\n    });\n  }\n}\n\n/**\n * Validates API key presence — returns Result for validate-style methods.\n * Use in adapter validateConfig() methods that return Result.\n */\nexport function validateApiKeyPresence(\n  apiKey: string | undefined,\n  providerId: string,\n  modelId: string\n): Result<void, ConfigError> {\n  if (isApiKeyMissing(apiKey)) {\n    return err(\n      new ConfigError(`${providerId} API key is required`, {\n        context: { providerId, modelId },\n      })\n    );\n  }\n  return ok(undefined);\n}\n\n/**\n * Abstract base class for model adapters.\n *\n * Provides default implementations for common adapter functionality while\n * leaving the core API interaction methods abstract for provider-specific\n * implementations.\n *\n * @example\n * ```typescript\n * class ClaudeAdapter extends BaseAdapter {\n *   constructor(config: ClaudeAdapterConfig) {\n *     super({\n *       providerId: 'anthropic',\n *       modelId: config.modelId,\n *       capabilities: [ModelCapability.COMPLETION, ModelCapability.STREAMING],\n *       apiKey: config.apiKey,\n *     });\n *   }\n *\n *   async complete(request: CompletionRequest): Promise<Result<CompletionResponse, ModelError>> {\n *     this.logRequest(request);\n *     // Provider-specific implementation...\n *   }\n *\n *   async *stream(request: CompletionRequest): AsyncIterable<StreamChunk> {\n *     this.logRequest(request);\n *     // Provider-specific streaming implementation...\n *   }\n * }\n * ```\n */\nexport abstract class BaseAdapter implements IModelAdapter {\n  readonly providerId: string;\n  readonly modelId: string;\n  readonly capabilities: readonly ModelCapability[];\n\n  /** Logger for request/response logging */\n  protected readonly logger: ILogger;\n\n  /** Configuration for the adapter */\n  protected readonly config: BaseAdapterConfig;\n\n  /**\n   * Creates a new BaseAdapter instance.\n   *\n   * @param config - Adapter configuration\n   */\n  constructor(config: BaseAdapterConfig) {\n    this.providerId = config.providerId;\n    this.modelId = config.modelId;\n    this.capabilities = config.capabilities;\n    this.config = config;\n    this.logger =\n      config.logger ??\n      createLogger({\n        adapter: config.providerId,\n        model: config.modelId,\n      });\n  }\n\n  /**\n   * Send a completion request to the model.\n   * Must be implemented by concrete adapter classes.\n   *\n   * @param request - The completion request\n   * @returns Result with response or ModelError\n   */\n  abstract complete(request: CompletionRequest): Promise<Result<CompletionResponse, ModelError>>;\n\n  /**\n   * Stream a completion request from the model.\n   * Must be implemented by concrete adapter classes.\n   *\n   * @param request - The completion request\n   * @yields StreamChunk objects as they arrive\n   */\n  abstract stream(request: CompletionRequest): AsyncIterable<StreamChunk>;\n\n  /**\n   * Count tokens in text using the unified TokenEstimator.\n   *\n   * This provides a reasonable estimate for most use cases.\n   * Concrete adapters may override this with provider-specific tokenizers.\n   *\n   * @param text - Text to count tokens for\n   * @returns Approximate token count\n   */\n  countTokens(text: string): Promise<number> {\n    return Promise.resolve(getTokenEstimator().estimateText(text));\n  }\n\n  /**\n   * Validate adapter configuration.\n   *\n   * Checks that required configuration fields are present and valid.\n   * Concrete adapters may override to add provider-specific validation.\n   *\n   * @returns Ok if valid, ConfigError if invalid\n   */\n  validateConfig(): Result<void, ConfigError> {\n    const errors: string[] = [];\n\n    if (!this.providerId || this.providerId.trim() === '') {\n      errors.push('Provider ID is required');\n    }\n\n    if (!this.modelId || this.modelId.trim() === '') {\n      errors.push('Model ID is required');\n    }\n\n    if (this.config.timeout !== undefined && this.config.timeout <= 0) {\n      errors.push('Timeout must be positive');\n    }\n\n    if (this.config.maxRetries !== undefined && this.config.maxRetries < 0) {\n      errors.push('Max retries cannot be negative');\n    }\n\n    if (errors.length > 0) {\n      return err(\n        new ConfigError(`Invalid adapter configuration: ${errors.join('; ')}`, {\n          context: {\n            providerId: this.providerId,\n            modelId: this.modelId,\n            errors,\n          },\n        })\n      );\n    }\n\n    return ok(undefined);\n  }\n\n  /**\n   * Check if this adapter supports a specific capability.\n   *\n   * @param capability - The capability to check for\n   * @returns True if the capability is supported\n   */\n  hasCapability(capability: ModelCapability): boolean {\n    return this.capabilities.includes(capability);\n  }\n\n  /**\n   * Log details about an outgoing request.\n   * Sanitizes sensitive information before logging.\n   *\n   * @param request - The completion request to log\n   */\n  protected logRequest(request: CompletionRequest): void {\n    const messageCount = request.messages.length;\n    const hasTools = request.tools !== undefined && request.tools.length > 0;\n    const toolCount = request.tools?.length ?? 0;\n\n    this.logger.debug('Sending completion request', {\n      messageCount,\n      hasSystemPrompt: request.systemPrompt !== undefined,\n      temperature: request.temperature,\n      maxTokens: request.maxTokens,\n      hasTools,\n      toolCount,\n      responseFormat: request.responseFormat?.type,\n      stopSequences: request.stop?.length ?? 0,\n    });\n  }\n\n  /**\n   * Log details about a received response.\n   *\n   * @param response - The completion response to log\n   */\n  protected logResponse(response: CompletionResponse): void {\n    this.logger.debug('Received completion response', {\n      contentBlocks: response.content.length,\n      stopReason: response.stopReason,\n      inputTokens: response.usage.inputTokens,\n      outputTokens: response.usage.outputTokens,\n      totalTokens: response.usage.totalTokens,\n      model: response.model,\n    });\n  }\n\n  /**\n   * Transform a provider-specific error into a standardized ModelError.\n   *\n   * Maps common error patterns to appropriate error codes:\n   * - Rate limiting (429, quota exceeded)\n   * - Timeouts (ETIMEDOUT, ESOCKETTIMEDOUT)\n   * - Authentication (401, 403)\n   * - Model unavailable (503, 502)\n   *\n   * @param error - The original error from the provider\n   * @returns A standardized ModelError\n   */\n  protected transformError(error: unknown): ModelError {\n    if (error instanceof ModelError) {\n      return error;\n    }\n\n    const errorMessage = getErrorMessage(error);\n    const errorCode = this.determineErrorCode(error);\n\n    const modelError = this.createModelError(errorMessage, errorCode, error);\n\n    this.logger.error('Model adapter error', modelError, {\n      errorCode,\n      providerId: this.providerId,\n      modelId: this.modelId,\n    });\n\n    return modelError;\n  }\n\n  /**\n   * Create a ModelError with appropriate error code.\n   */\n  private createModelError(\n    message: string,\n    errorCode: (typeof ErrorCode)[keyof typeof ErrorCode],\n    originalError: unknown\n  ): ModelError {\n    const fullMessage = `${this.providerId}/${this.modelId}: ${message}`;\n\n    // Build options object conditionally to satisfy exactOptionalPropertyTypes\n    const options: NexusErrorOptions = {\n      code: errorCode,\n      context: {\n        providerId: this.providerId,\n        modelId: this.modelId,\n      },\n    };\n\n    // Only set cause if originalError is an Error\n    if (originalError instanceof Error) {\n      options.cause = originalError;\n    }\n\n    // AdapterModelError extends ModelError — no cast needed\n    return new AdapterModelError(fullMessage, options);\n  }\n\n  /**\n   * Determine the appropriate error code based on error characteristics.\n   */\n  private determineErrorCode(error: unknown): (typeof ErrorCode)[keyof typeof ErrorCode] {\n    if (!(error instanceof Error)) {\n      return ErrorCode.MODEL_ERROR;\n    }\n\n    const message = error.message.toLowerCase();\n    const errorObj = error as { status?: number; code?: string };\n\n    // Check for rate limiting (canonical detection from rate-limit-detector)\n    if (isRateLimitLikeError(error)) {\n      return ErrorCode.MODEL_RATE_LIMITED;\n    }\n\n    // Check for timeout\n    if (this.isTimeoutError(message, errorObj)) {\n      return ErrorCode.MODEL_TIMEOUT;\n    }\n\n    // Check for model unavailable\n    if (this.isUnavailableError(message, errorObj)) {\n      return ErrorCode.MODEL_UNAVAILABLE;\n    }\n\n    return ErrorCode.MODEL_ERROR;\n  }\n\n  /**\n   * Check if error indicates a timeout.\n   */\n  private isTimeoutError(message: string, errorObj: { status?: number; code?: string }): boolean {\n    const timeoutPatterns = ['timeout', 'etimedout', 'esockettimedout'];\n    return (\n      errorObj.code === 'ETIMEDOUT' ||\n      errorObj.code === 'ESOCKETTIMEDOUT' ||\n      timeoutPatterns.some((pattern) => message.includes(pattern))\n    );\n  }\n\n  /**\n   * Check if error indicates model unavailability.\n   */\n  private isUnavailableError(\n    message: string,\n    errorObj: { status?: number; code?: string }\n  ): boolean {\n    const unavailablePatterns = ['unavailable', 'service unavailable', 'overloaded'];\n    return (\n      errorObj.status === 502 ||\n      errorObj.status === 503 ||\n      unavailablePatterns.some((pattern) => message.includes(pattern))\n    );\n  }\n}\n","/**\n * nexus-agents/adapters - Streaming Types and Core Utilities\n *\n * Shared types, errors, and core streaming primitives used by both\n * streaming.ts and stream-operators.ts to avoid circular dependencies.\n */\n\nimport { type Result, ok, err } from '../core/index.js';\nimport { NexusError, ErrorCode } from '../core/index.js';\n\n/**\n * Error thrown when a stream operation fails.\n */\nexport class StreamError extends NexusError {\n  constructor(message: string, options?: { cause?: Error; context?: Record<string, unknown> }) {\n    super(message, { code: ErrorCode.INTERNAL_ERROR, ...options });\n    this.name = 'StreamError';\n  }\n}\n\n/**\n * Error thrown when a stream is cancelled.\n */\nexport class StreamCancelledError extends NexusError {\n  constructor(reason?: string) {\n    super(reason ?? 'Stream was cancelled', { code: ErrorCode.INTERNAL_ERROR });\n    this.name = 'StreamCancelledError';\n  }\n}\n\n/**\n * State of a stream controller.\n */\nexport type StreamState = 'idle' | 'streaming' | 'paused' | 'cancelled' | 'completed' | 'error';\n\n/**\n * Options for creating a stream.\n */\nexport interface CreateStreamOptions {\n  /** AbortSignal for cancellation support */\n  signal?: AbortSignal;\n  /** Maximum buffer size for backpressure (default: 100) */\n  maxBufferSize?: number;\n}\n\n/**\n * Controller for managing stream lifecycle.\n * Provides push/complete/error methods and cancellation support.\n */\nexport class StreamController<T> {\n  private readonly chunks: T[] = [];\n  private readonly waiters: Array<{\n    resolve: (result: IteratorResult<T, void>) => void;\n    reject: (error: Error) => void;\n  }> = [];\n\n  private _state: StreamState = 'idle';\n  private _error: Error | undefined;\n  private readonly maxBufferSize: number;\n  private readonly abortHandler: (() => void) | undefined;\n  private readonly abortSignal: AbortSignal | undefined;\n\n  /**\n   * Creates a new StreamController.\n   * @param options - Stream creation options\n   */\n  constructor(options: CreateStreamOptions = {}) {\n    this.maxBufferSize = options.maxBufferSize ?? 100;\n\n    if (options.signal) {\n      this.abortSignal = options.signal;\n      this.abortHandler = (): void => {\n        this.cancel('AbortSignal triggered');\n      };\n      options.signal.addEventListener('abort', this.abortHandler);\n    }\n  }\n\n  /**\n   * Current state of the stream.\n   */\n  get state(): StreamState {\n    return this._state;\n  }\n\n  /**\n   * Whether the stream is still active (can receive chunks).\n   */\n  get isActive(): boolean {\n    return this._state === 'idle' || this._state === 'streaming' || this._state === 'paused';\n  }\n\n  /**\n   * Current buffer size.\n   */\n  get bufferSize(): number {\n    return this.chunks.length;\n  }\n\n  /**\n   * Push a chunk to the stream.\n   * @param chunk - The chunk to push\n   * @returns Result indicating success or backpressure\n   */\n  push(chunk: T): Result<void, StreamError> {\n    if (!this.isActive) {\n      return err(new StreamError(`Cannot push to stream in state: ${this._state}`));\n    }\n\n    if (this._state === 'idle') {\n      this._state = 'streaming';\n    }\n\n    // If there's a waiting consumer, deliver directly\n    const waiter = this.waiters.shift();\n    if (waiter) {\n      waiter.resolve({ done: false, value: chunk });\n      return ok(undefined);\n    }\n\n    // Check backpressure\n    if (this.chunks.length >= this.maxBufferSize) {\n      this._state = 'paused';\n      return err(\n        new StreamError('Buffer full - backpressure applied', {\n          context: { bufferSize: this.chunks.length, maxBufferSize: this.maxBufferSize },\n        })\n      );\n    }\n\n    this.chunks.push(chunk);\n    return ok(undefined);\n  }\n\n  /**\n   * Complete the stream successfully.\n   */\n  complete(): void {\n    if (!this.isActive) {\n      return;\n    }\n\n    this._state = 'completed';\n    this.removeAbortListener();\n    this.resolveAllWaiters();\n  }\n\n  /**\n   * Complete the stream with an error.\n   * @param error - The error that occurred\n   */\n  error(error: Error): void {\n    if (!this.isActive) {\n      return;\n    }\n\n    this._state = 'error';\n    this._error = error;\n    this.removeAbortListener();\n    this.rejectAllWaiters(error);\n  }\n\n  /**\n   * Cancel the stream.\n   * @param reason - Optional reason for cancellation\n   */\n  cancel(reason?: string): void {\n    if (!this.isActive) {\n      return;\n    }\n\n    this._state = 'cancelled';\n    this._error = new StreamCancelledError(reason);\n    this.removeAbortListener();\n    this.rejectAllWaiters(this._error);\n  }\n\n  /**\n   * Get the AsyncIterable for consuming the stream.\n   */\n  getIterable(): AsyncIterable<T> {\n    // Store reference to controller methods for closure\n    const nextChunk = (): Promise<IteratorResult<T, void>> => this.nextChunk();\n    const cancel = (reason: string): void => {\n      this.cancel(reason);\n    };\n\n    return {\n      [Symbol.asyncIterator](): AsyncIterator<T> {\n        return {\n          async next(): Promise<IteratorResult<T, void>> {\n            return nextChunk();\n          },\n          return(): Promise<IteratorResult<T, void>> {\n            cancel('Iterator returned');\n            return Promise.resolve({ done: true, value: undefined });\n          },\n        };\n      },\n    };\n  }\n\n  private async nextChunk(): Promise<IteratorResult<T, void>> {\n    // If we have buffered chunks, return one\n    const chunk = this.chunks.shift();\n    if (chunk !== undefined) {\n      // Resume if we were paused and buffer is now below threshold\n      if (this._state === 'paused' && this.chunks.length < this.maxBufferSize / 2) {\n        this._state = 'streaming';\n      }\n      return { done: false, value: chunk };\n    }\n\n    // Check terminal states\n    if (this._state === 'completed') {\n      return { done: true, value: undefined };\n    }\n\n    if (this._state === 'cancelled' || this._state === 'error') {\n      throw this._error ?? new StreamCancelledError();\n    }\n\n    // Wait for next chunk\n    return new Promise((resolve, reject) => {\n      this.waiters.push({ resolve, reject });\n    });\n  }\n\n  private removeAbortListener(): void {\n    if (this.abortSignal && this.abortHandler) {\n      this.abortSignal.removeEventListener('abort', this.abortHandler);\n    }\n  }\n\n  private resolveAllWaiters(): void {\n    for (const waiter of this.waiters) {\n      waiter.resolve({ done: true, value: undefined });\n    }\n    this.waiters.length = 0;\n  }\n\n  private rejectAllWaiters(error: Error): void {\n    for (const waiter of this.waiters) {\n      waiter.reject(error);\n    }\n    this.waiters.length = 0;\n  }\n}\n\n/**\n * Creates a controllable stream.\n * @param options - Stream creation options\n * @returns Tuple of [controller, iterable]\n */\nexport function createStream<T>(\n  options: CreateStreamOptions = {}\n): [StreamController<T>, AsyncIterable<T>] {\n  const controller = new StreamController<T>(options);\n  return [controller, controller.getIterable()];\n}\n","/**\n * nexus-agents/adapters - Stream Operators Helpers\n *\n * Helper functions for stream operations extracted for maintainability.\n */\n\nimport { type Result, ok, err } from '../core/index.js';\nimport { StreamError, StreamCancelledError } from './streaming-types.js';\n\n/**\n * Takes the first N chunks from a stream.\n * @param stream - The source stream\n * @param count - Number of chunks to take\n * @param options - Options including optional AbortSignal\n * @returns Stream of first N chunks\n */\nexport async function* take<T>(\n  stream: AsyncIterable<T>,\n  count: number,\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<T> {\n  if (count <= 0) {\n    return;\n  }\n\n  let taken = 0;\n\n  for await (const chunk of stream) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('take aborted');\n    }\n\n    yield chunk;\n    taken++;\n\n    if (taken >= count) {\n      return;\n    }\n  }\n}\n\n/**\n * Skips the first N chunks from a stream.\n * @param stream - The source stream\n * @param count - Number of chunks to skip\n * @param options - Options including optional AbortSignal\n * @returns Stream with first N chunks skipped\n */\nexport async function* skip<T>(\n  stream: AsyncIterable<T>,\n  count: number,\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<T> {\n  let skipped = 0;\n\n  for await (const chunk of stream) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('skip aborted');\n    }\n\n    if (skipped < count) {\n      skipped++;\n      continue;\n    }\n\n    yield chunk;\n  }\n}\n\n/**\n * Concatenates multiple streams sequentially.\n * @param streams - The streams to concatenate\n * @param options - Options including optional AbortSignal\n * @returns Concatenated stream\n */\nexport async function* concatStreams<T>(\n  streams: AsyncIterable<T>[],\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<T> {\n  for (const stream of streams) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('concat aborted');\n    }\n\n    yield* stream;\n  }\n}\n\n/**\n * Creates a stream from an array of values.\n * @param values - The values to stream\n * @param options - Options including optional delay between chunks\n * @returns Stream of values\n */\nexport async function* fromArray<T>(\n  values: T[],\n  options: { delayMs?: number; signal?: AbortSignal } = {}\n): AsyncIterable<T> {\n  for (const value of values) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('fromArray aborted');\n    }\n\n    if (options.delayMs !== undefined && options.delayMs > 0) {\n      await new Promise((resolve) => setTimeout(resolve, options.delayMs));\n    }\n\n    yield value;\n  }\n}\n\n/**\n * Taps into a stream without modifying it (for side effects like logging).\n * @param stream - The source stream\n * @param fn - Side effect function called for each chunk\n * @param options - Options including optional AbortSignal\n * @returns Original stream unchanged\n */\nexport async function* tapStream<T>(\n  stream: AsyncIterable<T>,\n  fn: (chunk: T, index: number) => void | Promise<void>,\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<T> {\n  let index = 0;\n\n  for await (const chunk of stream) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('tap aborted');\n    }\n\n    await fn(chunk, index);\n    yield chunk;\n    index++;\n  }\n}\n\n/**\n * Reduces a stream to a single value.\n * @param stream - The source stream\n * @param reducer - Reducer function\n * @param initialValue - Initial accumulator value\n * @param options - Options including optional AbortSignal\n * @returns Result containing the final value or error\n */\nexport async function reduceStream<T, U>(\n  stream: AsyncIterable<T>,\n  reducer: (accumulator: U, chunk: T, index: number) => U | Promise<U>,\n  initialValue: U,\n  options: { signal?: AbortSignal } = {}\n): Promise<Result<U, StreamError>> {\n  let accumulator = initialValue;\n  let index = 0;\n\n  try {\n    for await (const chunk of stream) {\n      if (options.signal?.aborted === true) {\n        return err(new StreamError('Reduce aborted'));\n      }\n\n      accumulator = await reducer(accumulator, chunk, index);\n      index++;\n    }\n\n    return ok(accumulator);\n  } catch (error) {\n    return err(\n      new StreamError('Failed to reduce stream', {\n        cause: error instanceof Error ? error : new Error(String(error)),\n      })\n    );\n  }\n}\n","/**\n * nexus-agents/adapters - Stream Operators\n *\n * Stream transformation operators for AsyncIterables.\n * Provides filter, map, merge, concat, buffer, and other stream operations.\n */\n\nimport { TimeoutError } from '../core/index.js';\nimport {\n  StreamError,\n  StreamCancelledError,\n  createStream,\n  type CreateStreamOptions,\n} from './streaming-types.js';\n\n// Re-export helper functions for backward compatibility\nexport {\n  take,\n  skip,\n  concatStreams,\n  fromArray,\n  tapStream,\n  reduceStream,\n} from './stream-operators-helpers.js';\n\n/**\n * Transforms stream chunks using a mapping function.\n * @param stream - The source stream\n * @param fn - Transformation function\n * @param options - Options including optional AbortSignal\n * @returns Transformed stream\n */\nexport async function* transformStream<T, U>(\n  stream: AsyncIterable<T>,\n  fn: (chunk: T, index: number) => U | Promise<U>,\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<U> {\n  let index = 0;\n\n  for await (const chunk of stream) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('Transform aborted');\n    }\n\n    yield await fn(chunk, index);\n    index++;\n  }\n}\n\n/**\n * Merges multiple streams into a single stream.\n * Chunks are yielded as they arrive from any source.\n * @param streams - The streams to merge\n * @param options - Options including optional AbortSignal\n * @returns Merged stream\n */\nexport async function* mergeStreams<T>(\n  streams: AsyncIterable<T>[],\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<T> {\n  if (streams.length === 0) {\n    return;\n  }\n\n  const streamOptions: CreateStreamOptions = {};\n  if (options.signal) {\n    streamOptions.signal = options.signal;\n  }\n  const [controller, merged] = createStream<T>(streamOptions);\n  let activeCount = streams.length;\n\n  // Start consuming all streams in parallel\n  const consumers = streams.map(async (stream, streamIndex) => {\n    try {\n      for await (const chunk of stream) {\n        if (options.signal?.aborted === true) {\n          break;\n        }\n        controller.push(chunk);\n      }\n    } catch (error) {\n      if (error instanceof StreamCancelledError) {\n        // Propagate cancellation\n        controller.cancel(`Stream ${String(streamIndex)} was cancelled`);\n        return;\n      }\n      controller.error(error instanceof Error ? error : new Error(String(error)));\n      return;\n    } finally {\n      activeCount--;\n      if (activeCount === 0) {\n        controller.complete();\n      }\n    }\n  });\n\n  // Start all consumers without blocking (Issue #541)\n  // Each consumer has try-catch that forwards errors to controller.error(),\n  // so Promise.all should always resolve. Add defensive catch for edge cases.\n  Promise.all(consumers).catch((error: unknown) => {\n    // This should not happen since each consumer catches its own errors,\n    // but handle it defensively to prevent silent failures.\n    controller.error(error instanceof Error ? error : new StreamError(String(error)));\n  });\n\n  yield* merged;\n}\n\n/**\n * Takes chunks from a stream until a predicate returns true.\n * @param stream - The source stream\n * @param predicate - Function that returns true to stop taking\n * @param options - Options including whether to include the matching chunk\n * @returns Stream of chunks up to (and optionally including) the match\n */\nexport async function* takeUntil<T>(\n  stream: AsyncIterable<T>,\n  predicate: (chunk: T, index: number) => boolean | Promise<boolean>,\n  options: { signal?: AbortSignal; inclusive?: boolean } = {}\n): AsyncIterable<T> {\n  let index = 0;\n\n  for await (const chunk of stream) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('takeUntil aborted');\n    }\n\n    const shouldStop = await predicate(chunk, index);\n\n    if (shouldStop) {\n      if (options.inclusive === true) {\n        yield chunk;\n      }\n      return;\n    }\n\n    yield chunk;\n    index++;\n  }\n}\n\n/**\n * Filters stream chunks based on a predicate.\n * @param stream - The source stream\n * @param predicate - Function that returns true to keep the chunk\n * @param options - Options including optional AbortSignal\n * @returns Filtered stream\n */\nexport async function* filterStream<T>(\n  stream: AsyncIterable<T>,\n  predicate: (chunk: T, index: number) => boolean | Promise<boolean>,\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<T> {\n  let index = 0;\n\n  for await (const chunk of stream) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('filter aborted');\n    }\n\n    if (await predicate(chunk, index)) {\n      yield chunk;\n    }\n\n    index++;\n  }\n}\n\n/**\n * Adds a timeout to a stream. If no chunk is received within the timeout,\n * the stream throws a TimeoutError.\n * @param stream - The source stream\n * @param timeoutMs - Timeout in milliseconds\n * @param options - Options including optional AbortSignal\n * @returns Stream with timeout applied\n */\nexport async function* withTimeout<T>(\n  stream: AsyncIterable<T>,\n  timeoutMs: number,\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<T> {\n  const iterator = stream[Symbol.asyncIterator]();\n\n  try {\n    let running = true;\n    while (running) {\n      if (options.signal?.aborted === true) {\n        throw new StreamCancelledError('withTimeout aborted');\n      }\n\n      let timeoutId: ReturnType<typeof setTimeout> | undefined;\n      try {\n        const result = await Promise.race([\n          iterator.next().then((res) => {\n            if (timeoutId !== undefined) {\n              clearTimeout(timeoutId);\n            }\n            return res;\n          }),\n          new Promise<never>((_, reject) => {\n            timeoutId = setTimeout(() => {\n              reject(\n                new TimeoutError(`Stream timed out after ${String(timeoutMs)}ms`, {\n                  context: { timeoutMs },\n                })\n              );\n            }, timeoutMs);\n          }),\n        ]);\n\n        if (result.done === true) {\n          running = false;\n        } else {\n          yield result.value;\n        }\n      } finally {\n        if (timeoutId !== undefined) {\n          clearTimeout(timeoutId);\n        }\n      }\n    }\n  } finally {\n    // Ensure the iterator is properly closed\n    if (iterator.return !== undefined) {\n      await iterator.return();\n    }\n  }\n}\n\n/**\n * Buffers stream chunks into groups of a specified size.\n * @param stream - The source stream\n * @param size - Buffer size\n * @param options - Options including optional AbortSignal\n * @returns Stream of chunk arrays\n */\nexport async function* bufferStream<T>(\n  stream: AsyncIterable<T>,\n  size: number,\n  options: { signal?: AbortSignal } = {}\n): AsyncIterable<T[]> {\n  if (size <= 0) {\n    throw new StreamError('Buffer size must be positive');\n  }\n\n  let buffer: T[] = [];\n\n  for await (const chunk of stream) {\n    if (options.signal?.aborted === true) {\n      throw new StreamCancelledError('buffer aborted');\n    }\n\n    buffer.push(chunk);\n\n    if (buffer.length >= size) {\n      yield buffer;\n      buffer = [];\n    }\n  }\n\n  // Yield remaining chunks\n  if (buffer.length > 0) {\n    yield buffer;\n  }\n}\n","/**\n * nexus-agents/adapters - Streaming Utilities\n *\n * AsyncIterator-based streaming utilities for model responses.\n * Provides stream creation, backpressure handling, cancellation support,\n * and chunk collection helpers.\n *\n * For stream transformation operators (map, filter, merge, etc.),\n * see ./stream-operators.ts\n */\n\nimport { type Result, ok, err } from '../core/index.js';\n\n// Re-export core streaming types and utilities from shared module\nexport {\n  StreamError,\n  StreamCancelledError,\n  StreamController,\n  createStream,\n  type StreamState,\n  type CreateStreamOptions,\n} from './streaming-types.js';\n\n// Import for use in this file\nimport { StreamError, StreamCancelledError } from './streaming-types.js';\n\n/**\n * Default cap on collected chunks — prevents unbounded memory growth when\n * callers forget to pass `maxChunks`. Callers that genuinely need no cap\n * must opt in explicitly with `{ maxChunks: Infinity }`. (#1913 Class F)\n */\nexport const DEFAULT_COLLECT_STREAM_MAX_CHUNKS = 100_000;\n\n/**\n * Collects all chunks from a stream into an array.\n *\n * @param stream - The stream to collect\n * @param options - Options including optional AbortSignal.\n *   `maxChunks` defaults to {@link DEFAULT_COLLECT_STREAM_MAX_CHUNKS} to\n *   prevent unbounded memory growth on forgotten limits. Pass\n *   `Infinity` explicitly for truly unbounded collection.\n * @returns Result containing collected chunks or error\n */\nexport async function collectStream<T>(\n  stream: AsyncIterable<T>,\n  options: { signal?: AbortSignal; maxChunks?: number } = {}\n): Promise<Result<T[], StreamError>> {\n  const chunks: T[] = [];\n  const maxChunks = options.maxChunks ?? DEFAULT_COLLECT_STREAM_MAX_CHUNKS;\n\n  try {\n    for await (const chunk of stream) {\n      if (options.signal?.aborted === true) {\n        return err(new StreamError('Collection aborted'));\n      }\n\n      chunks.push(chunk);\n\n      if (chunks.length >= maxChunks) {\n        break;\n      }\n    }\n\n    return ok(chunks);\n  } catch (error) {\n    if (error instanceof StreamCancelledError) {\n      return err(new StreamError('Stream was cancelled during collection', { cause: error }));\n    }\n    return err(\n      new StreamError('Failed to collect stream', {\n        cause: error instanceof Error ? error : new Error(String(error)),\n      })\n    );\n  }\n}\n\n// Re-export all stream operators for convenience\nexport {\n  transformStream,\n  mergeStreams,\n  takeUntil,\n  take,\n  skip,\n  filterStream,\n  withTimeout,\n  bufferStream,\n  concatStreams,\n  fromArray,\n  tapStream,\n  reduceStream,\n} from 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package/dist/{chunk-VGZJIR22.js → chunk-5WQ3SRSE.js}

@@ -2,7 +2,7 @@ import {
   ConfigError,
   err,
   ok
-} from "./chunk-7OBFO4GF.js";
+} from "./chunk-O4KUCF5S.js";
 
 // src/adapters/sdk/types.ts
 var PROVIDER_ENV_KEYS = {
@@ -117,4 +117,4 @@ export {
   CUSTOM_API_ALLOW_PRIVATE_ENV,
   validateCustomApiBaseUrl
 };
-//# sourceMappingURL=chunk-VGZJIR22.js.map
+//# sourceMappingURL=chunk-5WQ3SRSE.js.map

package/dist/{chunk-TOYPY5XA.js → chunk-A35XORXU.js}

@@ -4,13 +4,74 @@ import {
 import {
   ParseError,
   SecurityError,
-  getErrorMessage
-} from "./chunk-7OBFO4GF.js";
+  err,
+  getErrorMessage,
+  ok
+} from "./chunk-O4KUCF5S.js";
 
 // src/cli/research-helpers-io.ts
+import * as fs2 from "fs/promises";
+import { join, resolve as resolve2 } from "path";
+import { parse as parseYaml, stringify as stringifyYaml2 } from "yaml";
+
+// src/cli/research-scaffold.ts
 import * as fs from "fs/promises";
-import { join, resolve } from "path";
-import { parse as parseYaml, stringify as stringifyYaml } from "yaml";
+import { existsSync } from "fs";
+import { dirname, resolve } from "path";
+import { stringify as stringifyYaml } from "yaml";
+var SCHEMA_VERSION = "1.0";
+var ANNOUNCED = /* @__PURE__ */ new Set();
+function announceOnce(path, kind) {
+  if (ANNOUNCED.has(path)) return;
+  ANNOUNCED.add(path);
+  process.stderr.write(
+    `[scaffold] Created empty ${kind} at ${path}; add entries via 'nexus-agents research add' or research_add MCP tool.
+`
+  );
+}
+function scaffoldDisabled() {
+  const v = process.env["NEXUS_NO_SCAFFOLD"];
+  return v === "1" || v === "true";
+}
+function emptyPapersYaml() {
+  return stringifyYaml({ schema_version: SCHEMA_VERSION, papers: {} });
+}
+function emptyTechniquesYaml() {
+  return stringifyYaml({ schema_version: SCHEMA_VERSION, techniques: {} });
+}
+async function ensureRegistryFile(rootDir, filename) {
+  const filePath = resolve(rootDir, REGISTRY_PATH, filename);
+  if (existsSync(filePath)) return ok(filePath);
+  if (scaffoldDisabled()) {
+    return err(
+      new ParseError(
+        `Registry file missing: ${filePath}. Scaffolding disabled (NEXUS_NO_SCAFFOLD=1). Create the file manually or unset the env var.`
+      )
+    );
+  }
+  if (!existsSync(resolve(rootDir, "docs"))) {
+    return err(
+      new ParseError(
+        `Registry file missing: ${filePath}. ${rootDir}/docs/ does not exist; refusing to create a Nexus subtree in a non-documented root. Run 'nexus-agents init' first, or create ${rootDir}/docs/ manually.`
+      )
+    );
+  }
+  try {
+    await fs.mkdir(dirname(filePath), { recursive: true });
+    const content = filename === PAPERS_FILE ? emptyPapersYaml() : emptyTechniquesYaml();
+    await fs.writeFile(filePath, content, "utf-8");
+    announceOnce(filePath, filename);
+    return ok(filePath);
+  } catch (e) {
+    return err(
+      new ParseError(
+        `Failed to scaffold ${filename} at ${filePath}: ${getErrorMessage(e)}. Set NEXUS_NO_SCAFFOLD=1 and create manually if scaffolding is unwanted.`
+      )
+    );
+  }
+}
+
+// src/cli/research-helpers-io.ts
 var REGISTRY_PATH = "docs/research/registry";
 var TECHNIQUES_FILE = "techniques.yaml";
 var PAPERS_FILE = "papers.yaml";
@@ -23,7 +84,7 @@ function validatePath(constructedPath, allowedRoot) {
     return {
       ok: false,
       error: new SecurityError("Path traversal detected: path escapes allowed root directory", {
-        context: { constructedPath, allowedRoot: resolve(allowedRoot) }
+        context: { constructedPath, allowedRoot: resolve2(allowedRoot) }
       })
     };
   }
@@ -36,8 +97,9 @@ async function loadTechniquesRegistry(rootDir) {
   if (!pathValidation.ok) {
     return pathValidation;
   }
+  await ensureRegistryFile(root, TECHNIQUES_FILE);
   try {
-    const content = await fs.readFile(pathValidation.value, "utf-8");
+    const content = await fs2.readFile(pathValidation.value, "utf-8");
     return { ok: true, value: parseYaml(content) };
   } catch (error) {
     const message = getErrorMessage(error);
@@ -51,8 +113,9 @@ async function loadPapersRegistry(rootDir) {
   if (!pathValidation.ok) {
     return pathValidation;
   }
+  await ensureRegistryFile(root, PAPERS_FILE);
   try {
-    const content = await fs.readFile(pathValidation.value, "utf-8");
+    const content = await fs2.readFile(pathValidation.value, "utf-8");
     return { ok: true, value: parseYaml(content) };
   } catch (error) {
     const message = getErrorMessage(error);
@@ -67,8 +130,8 @@ async function savePapersRegistry(registry, rootDir) {
     return pathValidation;
   }
   try {
-    const content = stringifyYaml(registry, { lineWidth: 100 });
-    await fs.writeFile(pathValidation.value, content, "utf-8");
+    const content = stringifyYaml2(registry, { lineWidth: 100 });
+    await fs2.writeFile(pathValidation.value, content, "utf-8");
     return { ok: true, value: void 0 };
   } catch (error) {
     const message = getErrorMessage(error);
@@ -918,4 +981,4 @@ export {
   normalizeTopicToCanonical,
   synthesizeResearch
 };
-//# sourceMappingURL=chunk-TOYPY5XA.js.map
+//# sourceMappingURL=chunk-A35XORXU.js.map

package/dist/chunk-A35XORXU.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/research-helpers-io.ts","../src/cli/research-scaffold.ts","../src/cli/research-alignment-map.ts","../src/research/topic-aliases.ts","../src/cli/research-helpers-synthesize.ts"],"sourcesContent":["/**\n * Research Registry I/O Operations\n *\n * File operations for loading and saving research registry YAML files.\n * Includes path traversal protection per Issue #353.\n *\n * @see docs/research/RESEARCH_INDEX.md\n * @see Issue #237 (Epic #225)\n * @see Issue #353 (Security - Path traversal fix)\n */\n\nimport * as fs from 'node:fs/promises';\nimport { join, resolve } from 'node:path';\nimport { resolveInsideRoot } from '../security/safe-path.js';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport type { Result } from '../core/index.js';\nimport { SecurityError, getErrorMessage } from '../core/index.js';\nimport { ParseError } from '../core/types/workflow.js';\nimport type { TechniquesRegistry, PapersRegistry } from './research-types.js';\nimport { ensureRegistryFile } from './research-scaffold.js';\n\n// =============================================================================\n// CONSTANTS\n// =============================================================================\n\n/** Path to research registry directory relative to project root */\nexport const REGISTRY_PATH = 'docs/research/registry';\n\n/** Filename for techniques registry */\nexport const TECHNIQUES_FILE = 'techniques.yaml';\n\n/** Filename for papers registry */\nexport const PAPERS_FILE = 'papers.yaml';\n\n// =============================================================================\n// PROJECT ROOT\n// =============================================================================\n\n/**\n * Get the project root directory.\n * Note: Returns cwd since registry operations use explicit rootDir parameter\n */\nexport function getProjectRoot(): string {\n  return process.cwd();\n}\n\n// =============================================================================\n// PATH VALIDATION\n// =============================================================================\n\n/**\n * Validates that a constructed path stays within the allowed root directory.\n * Prevents path traversal attacks (e.g., ../../../etc/passwd).\n *\n * @param constructedPath - The full path to validate\n * @param allowedRoot - The root directory that paths must be within\n * @returns Result with validated absolute path or SecurityError\n */\nfunction validatePath(constructedPath: string, allowedRoot: string): Result<string, SecurityError> {\n  const resolved = resolveInsideRoot(constructedPath, allowedRoot);\n  if (resolved === null) {\n    return {\n      ok: false,\n      error: new SecurityError('Path traversal detected: path escapes allowed root directory', {\n        context: { constructedPath, allowedRoot: resolve(allowedRoot) },\n      }),\n    };\n  }\n  return { ok: true, value: resolved };\n}\n\n// =============================================================================\n// LOAD OPERATIONS\n// =============================================================================\n\n/**\n * Load techniques registry from YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with TechniquesRegistry or SecurityError/ParseError\n */\nexport async function loadTechniquesRegistry(\n  rootDir?: string\n): Promise<Result<TechniquesRegistry, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, TECHNIQUES_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  // #2470: try to scaffold an empty techniques.yaml on first run so research_*\n  // workflows don't error on a fresh install. No-op when file exists.\n  // When scaffold refuses (e.g. <rootDir>/docs/ doesn't exist, or\n  // NEXUS_NO_SCAFFOLD=1), fall through and let readFile produce the original\n  // ENOENT error — that's the existing contract.\n  await ensureRegistryFile(root, TECHNIQUES_FILE);\n\n  try {\n    const content = await fs.readFile(pathValidation.value, 'utf-8');\n    return { ok: true, value: parseYaml(content) as TechniquesRegistry };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to load techniques registry: ${message}`) };\n  }\n}\n\n/**\n * Load papers registry from YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with PapersRegistry or SecurityError/ParseError\n */\nexport async function loadPapersRegistry(\n  rootDir?: string\n): Promise<Result<PapersRegistry, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  // #2470: try to scaffold an empty papers.yaml on first run so research_*\n  // workflows don't error on a fresh install. No-op when file exists; falls\n  // through silently when scaffold refuses (no docs/ root, or NEXUS_NO_SCAFFOLD).\n  await ensureRegistryFile(root, PAPERS_FILE);\n\n  try {\n    const content = await fs.readFile(pathValidation.value, 'utf-8');\n    return { ok: true, value: parseYaml(content) as PapersRegistry };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to load papers registry: ${message}`) };\n  }\n}\n\n// =============================================================================\n// SAVE OPERATIONS\n// =============================================================================\n\n/**\n * Save techniques registry to YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param registry - The techniques registry to save\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with void on success or SecurityError/ParseError on failure\n */\nexport async function saveTechniquesRegistry(\n  registry: TechniquesRegistry,\n  rootDir?: string\n): Promise<Result<void, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, TECHNIQUES_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  try {\n    const content = stringifyYaml(registry, { lineWidth: 100 });\n    await fs.writeFile(pathValidation.value, content, 'utf-8');\n    return { ok: true, value: undefined };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to save techniques registry: ${message}`) };\n  }\n}\n\n/**\n * Save papers registry to YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param registry - The papers registry to save\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with void on success or SecurityError/ParseError on failure\n */\nexport async function savePapersRegistry(\n  registry: PapersRegistry,\n  rootDir?: string\n): Promise<Result<void, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  try {\n    const content = stringifyYaml(registry, { lineWidth: 100 });\n    await fs.writeFile(pathValidation.value, content, 'utf-8');\n    return { ok: true, value: undefined };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to save papers registry: ${message}`) };\n  }\n}\n","/**\n * research-scaffold — auto-create empty research registry files when missing.\n *\n * On a fresh install or in a sandboxed environment where the project doesn't\n * have `docs/research/registry/`, the research workflows previously errored\n * with `Failed to load papers registry: ENOENT`. The user has no idea what\n * to do.\n *\n * This module provides `ensureResearchRegistry()`: idempotent scaffolding\n * that creates empty YAML registries on ENOENT, announces what it did to\n * stderr (so the operator knows), and returns the path that's now safe to\n * read.\n *\n * Source: Issue #2470 (epic #2467 child).\n */\n\nimport * as fs from 'node:fs/promises';\nimport { existsSync } from 'node:fs';\nimport { dirname, resolve } from 'node:path';\nimport { stringify as stringifyYaml } from 'yaml';\n\nimport type { Result } from '../core/index.js';\nimport { ok, err, getErrorMessage } from '../core/index.js';\nimport { ParseError } from '../core/types/workflow.js';\n\nimport { REGISTRY_PATH, PAPERS_FILE, TECHNIQUES_FILE } from './research-helpers-io.js';\n\n/**\n * Names of the registry files this scaffolder knows how to create.\n * `sources.yaml` and `alignments.yaml` live alongside but are populated by\n * different code paths; this scaffolder only owns the two YAML registries\n * that block `research_query` / `research_synthesize` on a fresh install.\n */\ntype ScaffoldedFile = typeof PAPERS_FILE | typeof TECHNIQUES_FILE;\n\nconst SCHEMA_VERSION = '1.0';\n\nconst ANNOUNCED = new Set<string>();\n\nfunction announceOnce(path: string, kind: ScaffoldedFile): void {\n  // De-dupe so that running multiple research commands in one session\n  // produces one announcement per scaffolded file, not per call.\n  if (ANNOUNCED.has(path)) return;\n  ANNOUNCED.add(path);\n  process.stderr.write(\n    `[scaffold] Created empty ${kind} at ${path}; add entries via 'nexus-agents research add' or research_add MCP tool.\\n`\n  );\n}\n\n/**\n * Operator opt-out. When set, scaffolding errors loudly with an actionable\n * message instead of silently writing files. Useful for CI and for\n * environments that want strict \"fail when state is wrong\" semantics.\n */\nfunction scaffoldDisabled(): boolean {\n  const v = process.env['NEXUS_NO_SCAFFOLD'];\n  return v === '1' || v === 'true';\n}\n\nfunction emptyPapersYaml(): string {\n  return stringifyYaml({ schema_version: SCHEMA_VERSION, papers: {} });\n}\n\nfunction emptyTechniquesYaml(): string {\n  return stringifyYaml({ schema_version: SCHEMA_VERSION, techniques: {} });\n}\n\n/**\n * Create the registry directory + an empty YAML file if either is missing.\n * Idempotent: existing files are left untouched.\n *\n * Scaffolds only when `<rootDir>/docs/` already exists. That guard keeps\n * tests, vitest's package cwd, and random scratch directories from getting\n * a `docs/research/` subtree implicitly. Operators on a real project root\n * (which always has `docs/`, either from cloning the repo or running\n * `nexus-agents init`) still get the auto-create behavior the issue asks for.\n *\n * Returns the resolved file path on success, or a ParseError when scaffolding\n * is disabled / refused (so the caller can pass the error through unchanged\n * for backwards compat with existing call sites).\n */\nexport async function ensureRegistryFile(\n  rootDir: string,\n  filename: ScaffoldedFile\n): Promise<Result<string, ParseError>> {\n  const filePath = resolve(rootDir, REGISTRY_PATH, filename);\n\n  if (existsSync(filePath)) return ok(filePath);\n\n  if (scaffoldDisabled()) {\n    return err(\n      new ParseError(\n        `Registry file missing: ${filePath}. Scaffolding disabled (NEXUS_NO_SCAFFOLD=1). Create the file manually or unset the env var.`\n      )\n    );\n  }\n\n  // Refuse to create a docs/ subtree in directories that aren't already\n  // documented project roots. The presence of `<rootDir>/docs/` is the\n  // strong signal we use.\n  if (!existsSync(resolve(rootDir, 'docs'))) {\n    return err(\n      new ParseError(\n        `Registry file missing: ${filePath}. ${rootDir}/docs/ does not exist; ` +\n          `refusing to create a Nexus subtree in a non-documented root. ` +\n          `Run 'nexus-agents init' first, or create ${rootDir}/docs/ manually.`\n      )\n    );\n  }\n\n  try {\n    await fs.mkdir(dirname(filePath), { recursive: true });\n    const content = filename === PAPERS_FILE ? emptyPapersYaml() : emptyTechniquesYaml();\n    await fs.writeFile(filePath, content, 'utf-8');\n    announceOnce(filePath, filename);\n    return ok(filePath);\n  } catch (e: unknown) {\n    return err(\n      new ParseError(\n        `Failed to scaffold ${filename} at ${filePath}: ${getErrorMessage(e)}. Set NEXUS_NO_SCAFFOLD=1 and create manually if scaffolding is unwanted.`\n      )\n    );\n  }\n}\n\n/**\n * Convenience: scaffold both papers.yaml and techniques.yaml. Used by the\n * research workflow startup paths that need both registries available.\n */\nexport async function ensureResearchRegistry(rootDir?: string): Promise<Result<void, ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const papers = await ensureRegistryFile(root, PAPERS_FILE);\n  if (!papers.ok) return papers;\n  const techniques = await ensureRegistryFile(root, TECHNIQUES_FILE);\n  if (!techniques.ok) return techniques;\n  return ok(undefined);\n}\n\n/**\n * Test-only reset of the announcement de-dupe set. Production code never\n * needs this; tests do because Vitest reuses process state across files.\n */\nexport function _resetAnnouncedForTests(): void {\n  ANNOUNCED.clear();\n}\n","/**\n * Research Alignment Map\n *\n * Maps technique names from the research registry to canonical code paths\n * in the nexus-agents codebase. Used by research synthesis to determine\n * which paper techniques are implemented, partially implemented, or new.\n *\n * @module cli/research-alignment-map\n * (Source: Issue #1386 — Research Synthesis Pipeline)\n */\n\n// =============================================================================\n// TYPES\n// =============================================================================\n\n/** Implementation status for a mapped technique. */\nexport interface TechniqueMapping {\n  readonly status: 'implemented' | 'partial';\n  readonly path: string;\n  readonly hint?: string | undefined;\n}\n\n/** A feature gate that controls an implementation. */\nexport interface FeatureGate {\n  /** Environment variable or config key. */\n  readonly envVar: string;\n  /** Default value when not explicitly set. */\n  readonly defaultValue: string;\n  /** Brief description of what the gate controls. */\n  readonly description: string;\n  /** Related technique names from the alignment map (if any). */\n  readonly techniques?: readonly string[];\n}\n\n// =============================================================================\n// MAP\n// =============================================================================\n\n/**\n * Maps technique names to canonical code paths.\n * 'implemented' = full implementation exists matching the technique.\n * 'partial' = related code exists but doesn't fully implement the technique.\n */\nexport const TECHNIQUE_IMPLEMENTATION_MAP: ReadonlyMap<string, TechniqueMapping> = new Map([\n  // Routing techniques\n  ['linucb-routing', { status: 'implemented', path: 'cli-adapters/linucb-bandit.ts' }],\n  ['topsis-routing', { status: 'implemented', path: 'cli-adapters/topsis-router.ts' }],\n  [\n    'cascade-routing',\n    { status: 'implemented', path: 'routing/stages/confidence-cascade-stage.ts' },\n  ],\n  [\n    'complexity-based-routing',\n    { status: 'implemented', path: 'routing/stages/confidence-cascade-stage.ts' },\n  ],\n  [\n    'moe-routing',\n    {\n      status: 'implemented',\n      path: 'cli-adapters/composite-router.ts',\n      hint: '5-stage composite routing selects among specialized CLI experts based on task features',\n    },\n  ],\n  ['two-stage-routing', { status: 'implemented', path: 'cli-adapters/composite-router-stages.ts' }],\n  [\n    'capability-instruction-tuning',\n    {\n      status: 'partial',\n      path: 'routing/stages/capability-match-stage.ts',\n      hint: 'Static capability profiles, not instruction-tuned',\n    },\n  ],\n  [\n    'knn-routing',\n    {\n      status: 'implemented',\n      path: 'routing/stages/knn-routing-stage.ts',\n      hint: 'KnnRoutingStage: cosine similarity over keyword vectors, K-nearest experience patterns, weighted by success rate',\n    },\n  ],\n  ['pilot-budget-routing', { status: 'implemented', path: 'cli-adapters/budget-router.ts' }],\n  [\n    'tolerance-routing',\n    {\n      status: 'implemented',\n      path: 'cli-adapters/composite-router-helpers.ts',\n      hint: 'TOPSIS_TOLERANCE_BAND_PERCENT (5%) identifies quality-equivalent candidates after TOPSIS ranking',\n    },\n  ],\n  [\n    'sater-routing',\n    {\n      status: 'implemented',\n      path: 'routing/stages/quality-constraint-stage.ts',\n      hint: 'QualityConstraintStage filters models by min quality (0.7), max cost, max latency before selection',\n    },\n  ],\n  [\n    'preference-trained-routing',\n    { status: 'implemented', path: 'cli-adapters/preference-router.ts' },\n  ],\n  [\n    'strmac-state-routing',\n    {\n      status: 'implemented',\n      path: 'context/routing-memory.ts',\n      hint: 'RoutingMemory maintains state across calls (profile, experience, action cache) feeding LinUCB + weather bonus stages',\n    },\n  ],\n  [\n    'cross-attention-routing',\n    {\n      status: 'implemented',\n      path: 'routing/stages/capability-match-stage.ts',\n      hint: 'AttentionMatrix maps task features to capability weights (configurable cross-attention)',\n    },\n  ],\n\n  // Consensus techniques\n  ['consensus-protocol', { status: 'implemented', path: 'consensus/engine.ts' }],\n  ['majority-voting', { status: 'implemented', path: 'consensus/engine.ts' }],\n  ['higher-order-voting', { status: 'implemented', path: 'consensus/higher-order-strategy.ts' }],\n  [\n    'anti-conformity-weighting',\n    { status: 'implemented', path: 'consensus/higher-order-strategy.ts' },\n  ],\n  [\n    'agreement-based-cascading',\n    {\n      status: 'implemented',\n      path: 'consensus/engine.ts',\n      hint: 'canCascadeEarly() closes proposals when outcome is mathematically determined',\n    },\n  ],\n  [\n    'incremental-quorum',\n    {\n      status: 'implemented',\n      path: 'consensus/incremental-quorum.ts',\n      hint: 'Ambiguity detection + voter expansion via VoterExpansionCallback (#1408)',\n    },\n  ],\n  [\n    'aegean-consensus',\n    { status: 'partial', path: 'consensus/engine.ts', hint: 'Byzantine tolerance not implemented' },\n  ],\n  [\n    'cp-wbft-consensus',\n    {\n      status: 'partial',\n      path: 'consensus/engine.ts',\n      hint: 'No weighted Byzantine fault tolerance',\n    },\n  ],\n\n  // Memory techniques\n  ['adaptive-memory', { status: 'implemented', path: 'memory/adaptive/' }],\n  ['mirix-six-type-memory', { status: 'implemented', path: 'memory/typed/' }],\n  [\n    'mem0-memory-architecture',\n    { status: 'partial', path: 'memory/', hint: 'Multi-backend memory but not mem0 pattern' },\n  ],\n  [\n    'graph-based-memory',\n    {\n      status: 'partial',\n      path: 'memory/belief/',\n      hint: 'Belief triples are graph-like but not full graph DB',\n    },\n  ],\n  ['experience-memory', { status: 'implemented', path: 'memory/session/' }],\n  ['hindsight-belief-memory', { status: 'implemented', path: 'memory/belief/' }],\n  [\n    'profile-memory',\n    {\n      status: 'implemented',\n      path: 'context/routing-memory.ts',\n      hint: 'RoutingMemory stores model preferences per task type and feeds recommendations into composite router via PERSISTENCE_AWARE_FLAGS',\n    },\n  ],\n  [\n    'action-memory',\n    {\n      status: 'implemented',\n      path: 'orchestration/outcomes/',\n      hint: 'OutcomeStore records actions+results+context with query-by-category/CLI/time and cross-session persistence',\n    },\n  ],\n  ['reflection-memory', { status: 'implemented', path: 'mcp/tools/orchestrate-reflection.ts' }],\n  [\n    'history-encoding',\n    {\n      status: 'partial',\n      path: 'context/token-counter.ts',\n      hint: 'Token counting exists but no learned history encoding',\n    },\n  ],\n\n  // Orchestration techniques\n  [\n    'aflow-mcts-workflows',\n    {\n      status: 'partial',\n      path: 'workflows/aflow/',\n      hint: 'AFlow scaffolding exists but MCTS not implemented',\n    },\n  ],\n  [\n    'dynamic-agent-selection',\n    { status: 'implemented', path: 'orchestration/aorchestra/agent-planner.ts' },\n  ],\n  ['dynamic-subagent-creation', { status: 'implemented', path: 'mcp/tools/create-expert.ts' }],\n  ['role-based-protocols', { status: 'implemented', path: 'agents/expert-roles.ts' }],\n  [\n    'rule-based-coordination',\n    { status: 'implemented', path: 'orchestration/aorchestra/worker-dispatcher.ts' },\n  ],\n  [\n    'temporal-graph-orchestration',\n    {\n      status: 'partial',\n      path: 'orchestration/graph/',\n      hint: 'Graph workflows exist but not temporal-aware',\n    },\n  ],\n  [\n    'model-based-coordination',\n    {\n      status: 'partial',\n      path: 'orchestration/aorchestra/',\n      hint: 'Worker dispatch but not model-based coordination theory',\n    },\n  ],\n  [\n    'trinity-roles',\n    {\n      status: 'partial',\n      path: 'agents/expert-roles.ts',\n      hint: '10 expert roles, not trinity pattern',\n    },\n  ],\n  [\n    'sew-self-evolving-workflows',\n    {\n      status: 'partial',\n      path: 'workflows/aflow/',\n      hint: 'AFlow framework but no self-evolution loop',\n    },\n  ],\n  [\n    'scaling-coordination-predictor',\n    {\n      status: 'partial',\n      path: 'orchestration/aorchestra/agent-planner.ts',\n      hint: 'Wave sizing but no scaling prediction',\n    },\n  ],\n\n  // Learning techniques\n  [\n    'self-refine-loop',\n    {\n      status: 'implemented',\n      path: 'mcp/tools/orchestrate-dispatch.ts',\n    },\n  ],\n  [\n    'recursive-improvement',\n    {\n      status: 'implemented',\n      path: 'mcp/tools/orchestrate-dispatch.ts',\n    },\n  ],\n  [\n    'rl-orchestrator',\n    {\n      status: 'implemented',\n      path: 'cli-adapters/linucb-bandit.ts',\n      hint: 'LinUCB contextual bandit actively selects models via explore-exploit in routing pipeline',\n    },\n  ],\n  ['reflexion-verbal-rl', { status: 'implemented', path: 'mcp/tools/orchestrate-reflection.ts' }],\n\n  // Source-derived techniques (Wave 6 — from open-source project analysis)\n  ['failure-lesson-injection', { status: 'implemented', path: 'orchestration/failure-lessons.ts' }],\n  [\n    'skill-relevance-matching',\n    {\n      status: 'implemented',\n      path: 'agents/experts/skill-matcher.ts',\n      hint: 'Matches task keywords to agent skill descriptions for optimal routing',\n    },\n  ],\n  [\n    'context-rot-prevention',\n    {\n      status: 'implemented',\n      path: 'agents/context-pruner.ts',\n      hint: 'Token-efficient context pruning prevents quality degradation in long sessions',\n    },\n  ],\n  [\n    'wave-based-parallel-execution',\n    {\n      status: 'implemented',\n      path: 'orchestration/aorchestra/worker-dispatcher.ts',\n      hint: 'AOrchestra worker dispatch with cross-wave context sharing',\n    },\n  ],\n  [\n    'write-time-deduplication',\n    {\n      status: 'implemented',\n      path: 'mcp/tools/memory-write.ts',\n      hint: 'Semantic dedup at write time prevents memory bloat',\n    },\n  ],\n]);\n\n// =============================================================================\n// FEATURE GATE INVENTORY\n// =============================================================================\n\n/** Inventory of feature gates linked to research-aligned techniques. */\nexport const FEATURE_GATE_INVENTORY: readonly FeatureGate[] = [\n  {\n    envVar: 'NEXUS_V2_MODE',\n    defaultValue: 'full',\n    description: 'V2 pipeline mode (off/partial/full)',\n    techniques: ['two-stage-routing', 'cascade-routing'],\n  },\n  {\n    envVar: 'NEXUS_AORCHESTRA',\n    defaultValue: 'true',\n    description: 'AOrchestra dynamic agent planning',\n    techniques: ['dynamic-agent-selection', 'model-based-coordination'],\n  },\n  {\n    envVar: 'NEXUS_AORCHESTRA_DISPATCH',\n    defaultValue: 'true',\n    description: 'AOrchestra worker dispatch',\n    techniques: ['rule-based-coordination', 'self-refine-loop'],\n  },\n  {\n    envVar: 'NEXUS_PERSIST_LEARNING',\n    defaultValue: 'true',\n    description: 'Cross-session routing persistence',\n    techniques: ['linucb-routing', 'preference-trained-routing', 'experience-memory'],\n  },\n  {\n    envVar: 'NEXUS_REFLECTIVE_MEMORY',\n    defaultValue: 'shadow',\n    description: 'Reflective memory retrieval (shadow=default, true=full, false=off)',\n    techniques: ['reflection-memory', 'adaptive-memory', 'reflexion-verbal-rl'],\n  },\n  {\n    envVar: 'NEXUS_BILLING_MODE',\n    defaultValue: 'plan',\n    description: 'Cost mode (plan=strongest, api=cost-aware)',\n    techniques: ['pilot-budget-routing', 'topsis-routing'],\n  },\n  {\n    envVar: 'NEXUS_WORKER_MAX_CALLS',\n    defaultValue: '6',\n    description: 'Max model calls per orchestrate',\n    techniques: ['self-refine-loop', 'recursive-improvement'],\n  },\n  { envVar: 'NEXUS_AUTH_ENABLED', defaultValue: 'true', description: 'Server authentication' },\n  { envVar: 'NEXUS_EVENTBUS_ENABLED', defaultValue: 'true', description: 'EventBus A2A bridge' },\n  {\n    envVar: 'NEXUS_RATE_LIMIT_ENABLED',\n    defaultValue: 'true',\n    description: 'Token-bucket rate limiter',\n  },\n  {\n    envVar: 'NEXUS_CIRCUIT_BREAKER_THRESHOLD',\n    defaultValue: '5',\n    description: 'Circuit breaker failure threshold',\n  },\n  {\n    envVar: 'NEXUS_V2_POLICY_MODE',\n    defaultValue: 'block',\n    description: 'Policy enforcement (off/warn/block)',\n  },\n  { envVar: 'NEXUS_LOG_LEVEL', defaultValue: 'info', description: 'Logging verbosity' },\n  {\n    envVar: 'NEXUS_DISABLE_SESSIONS',\n    defaultValue: 'false',\n    description: 'Disable session tracking',\n  },\n  {\n    envVar: 'NEXUS_DISABLE_METRICS',\n    defaultValue: 'false',\n    description: 'Disable metrics tracking',\n  },\n  {\n    envVar: 'NEXUS_ALLOW_MOCK_ORCHESTRATION',\n    defaultValue: 'false',\n    description: 'Allow mock orchestration (test/CI)',\n  },\n  {\n    envVar: 'NEXUS_MAX_CONCURRENT_EXPERTS',\n    defaultValue: '6',\n    description: 'Expert pool semaphore capacity',\n  },\n  {\n    envVar: 'NEXUS_VOTE_TIMEOUT_MS',\n    defaultValue: '60000',\n    description: 'Consensus vote timeout override',\n  },\n  {\n    envVar: 'NEXUS_EXPERT_TIMEOUT_MS',\n    defaultValue: '120000',\n    description: 'Expert handler timeout override',\n  },\n  {\n    envVar: 'NEXUS_WORKER_TIMEOUT_MS',\n    defaultValue: '60000',\n    description: 'Worker subprocess timeout override',\n  },\n];\n","/**\n * Topic alias map for normalizing free-form topic strings to canonical topics.\n *\n * Maps 200+ free-form topic strings found in papers.yaml to 12 canonical topics.\n * Used by normalizeTopicToCanonical() in research-schemas.ts.\n *\n * @module research/topic-aliases\n * @see Issue #1578 — Topic taxonomy normalization\n */\n\n/**\n * Map of free-form topic strings to canonical topics.\n */\nexport const TOPIC_ALIASES: Readonly<Record<string, string>> = {\n  // → consensus\n  voting: 'consensus',\n  'consensus-voting': 'consensus',\n  debate: 'consensus',\n  quorum: 'consensus',\n  byzantine: 'consensus',\n  'anti-conformity': 'consensus',\n  'agreement-based': 'consensus',\n  'correlation-aware': 'consensus',\n  'LLM consensus and multi-agent voting mechanisms': 'consensus',\n  'tolerance-parameter': 'consensus',\n\n  // → routing\n  'model-routing': 'routing',\n  'model routing': 'routing',\n  'llm-routing': 'routing',\n  cascade: 'routing',\n  'cascade-routing': 'routing',\n  'cost-optimization': 'routing',\n  'cost-reduction': 'routing',\n  'model-selection': 'routing',\n  topsis: 'routing',\n  linucb: 'routing',\n  'contextual-bandit': 'routing',\n  'quality-constrained': 'routing',\n  'budget-constraints': 'routing',\n  'unified-routing': 'routing',\n  'query-model-matching': 'routing',\n  'adaptive model routing and selection optimization': 'routing',\n  'multi-model routing optimization': 'routing',\n  'Single-head cross-attention for query-model matching': 'routing',\n  'performance-cost-tradeoff': 'routing',\n  'task-routing': 'routing',\n  'difficulty-estimation': 'routing',\n  'score-based': 'routing',\n  'optimal-weighting': 'routing',\n  'hierarchical-filtering': 'routing',\n  'preference-optimization': 'routing',\n  'preference-data': 'routing',\n  dpo: 'routing',\n  'cross-attention': 'routing',\n  'cma-es': 'routing',\n  profile: 'routing',\n  prediction: 'routing',\n  lightweight: 'routing',\n  bayesian: 'routing',\n  'quality-diversity': 'routing',\n  'resource-optimization': 'routing',\n  'routing-latency': 'routing',\n  optimization: 'routing',\n  'model-merging': 'routing',\n  'model-zoo': 'routing',\n\n  // → memory\n  'context-management': 'memory',\n  'context-compression': 'memory',\n  'context-control': 'memory',\n  compression: 'memory',\n  'kv-cache': 'memory',\n  'long-context': 'memory',\n  'long-term-memory': 'memory',\n  'episodic-memory': 'memory',\n  'graph-memory': 'memory',\n  'hierarchical-memory': 'memory',\n  'agentic-memory': 'memory',\n  'lifelong-learning': 'memory',\n  'cross-session-learning': 'memory',\n  'continual-learning': 'memory',\n  'self-editing-memory': 'memory',\n  'six-type-memory': 'memory',\n  'belief-memory': 'memory',\n  'belief-state': 'memory',\n  'action-memory': 'memory',\n  'memory-evolution': 'memory',\n  'virtual-context': 'memory',\n  paging: 'memory',\n  'prompt-compression': 'memory',\n  'learned-compression': 'memory',\n  zettelkasten: 'memory',\n  'knowledge-distillation': 'memory',\n  'history-encoding': 'memory',\n  'ictm-tuple': 'memory',\n  'latent-space': 'memory',\n  'vector-db': 'memory',\n  embedding: 'memory',\n  'Taxonomy of context management strategies': 'memory',\n  'Task-specific context compression': 'memory',\n  'Learned compression modules': 'memory',\n  rag: 'memory',\n  'retrieval augmented generation': 'memory',\n  svd: 'memory',\n  'svd-mutation': 'memory',\n  vae: 'memory',\n  knn: 'memory',\n  experience: 'memory',\n  'state-aware': 'memory',\n  'temporal-graph': 'memory',\n  versioning: 'memory',\n\n  // → code-generation\n  'code-repair': 'code-generation',\n  'code-agent': 'code-generation',\n  'code-review': 'code-generation',\n  'software-engineering': 'code-generation',\n  'swe-bench': 'code-generation',\n  'self-improvement': 'code-generation',\n  'self-evolving': 'code-generation',\n  'self-debug': 'code-generation',\n  'self-modification': 'code-generation',\n  'skill-library': 'code-generation',\n  'skill-discovery': 'code-generation',\n  'code review benchmarks': 'code-generation',\n  'code generation evaluation': 'code-generation',\n  'execution-feedback': 'code-generation',\n\n  // → cli-tools\n  mcp: 'cli-tools',\n  'MCP protocol': 'cli-tools',\n  'MCP security': 'cli-tools',\n  'MCP Security': 'cli-tools',\n  'mcp-applications': 'cli-tools',\n  'model-context-protocol': 'cli-tools',\n  puppeteer: 'cli-tools',\n  streaming: 'cli-tools',\n  integration: 'cli-tools',\n\n  // → orchestration\n  'multi-agent': 'orchestration',\n  'multi-agent-systems': 'orchestration',\n  'multi-agent orchestration': 'orchestration',\n  'Multi-Agent Orchestration': 'orchestration',\n  'multi-agent-orchestration': 'orchestration',\n  'multi-agent coordination': 'orchestration',\n  'multi-agent-coordination': 'orchestration',\n  'multi-agent-worker-dispatch': 'orchestration',\n  'multi-agent reliability': 'orchestration',\n  'multi-agent-rl': 'orchestration',\n  coordination: 'orchestration',\n  coordinator: 'orchestration',\n  collaboration: 'orchestration',\n  'graph-orchestration': 'orchestration',\n  'agent architecture': 'orchestration',\n  'dynamic-agent-creation': 'orchestration',\n  'specialized-agents': 'orchestration',\n  'thinker-worker-verifier': 'orchestration',\n  'two-agent': 'orchestration',\n  'meta-agent': 'orchestration',\n  agents: 'orchestration',\n  'workflow-optimization': 'orchestration',\n  'workflow-generation': 'orchestration',\n  'agent-communication': 'orchestration',\n  'inter-agent': 'orchestration',\n  'gvu-operator': 'orchestration',\n  'rubber-duck': 'orchestration',\n  'parallel-exploration': 'orchestration',\n  kubernetes: 'orchestration',\n  'scale-to-zero': 'orchestration',\n  edge: 'orchestration',\n  llm: 'orchestration',\n  multimodal: 'orchestration',\n  production: 'orchestration',\n  hybrid: 'orchestration',\n  'automatic-discovery': 'orchestration',\n  roadmap: 'orchestration',\n\n  // → security\n  'prompt injection defense': 'security',\n  'inter-agent-security': 'security',\n  'agent security': 'security',\n  compliance: 'security',\n  'formal-verification': 'security',\n  'formal-safety': 'security',\n\n  // → evaluation\n  benchmark: 'evaluation',\n  benchmarking: 'evaluation',\n  survey: 'evaluation',\n  'autonomous agent evaluation benchmarks': 'evaluation',\n  'evaluation-methods': 'evaluation',\n  'LLM evaluation': 'evaluation',\n  'hallucination-detection': 'evaluation',\n  'self-evaluation': 'evaluation',\n  'confidence-probe': 'evaluation',\n  'confidence-aware': 'evaluation',\n  verifier: 'evaluation',\n  observability: 'evaluation',\n  theoretical: 'evaluation',\n  'post-deployment': 'evaluation',\n  capability: 'evaluation',\n  'knowledge-gaps': 'evaluation',\n  helm: 'evaluation',\n\n  // → safety\n  'agentic-safety': 'safety',\n  'agentic AI safety': 'safety',\n  'safety-evaluation': 'safety',\n  'reward-modeling': 'safety',\n  'constitutional-ai': 'safety',\n  'hazard-analysis': 'safety',\n  stpa: 'safety',\n  'risk-assessment': 'safety',\n  'fault-tolerance': 'safety',\n  'ai-feedback': 'safety',\n  rlaif: 'safety',\n  'human-in-the-loop': 'safety',\n  feedback: 'safety',\n  'feedback-loop': 'safety',\n  'feedback-learning': 'safety',\n  anthropic: 'safety',\n\n  // → planning\n  'decision-making': 'planning',\n  'tree-search': 'planning',\n  'tree-structure': 'planning',\n  'multi-tree': 'planning',\n  mcts: 'planning',\n  backtrack: 'planning',\n  hindsight: 'planning',\n  'task-specific': 'planning',\n\n  // → tool-use\n  'tool use': 'tool-use',\n  'tool-augmented reasoning and function calling': 'tool-use',\n  'tool routing optimization': 'tool-use',\n  'dynamic-linking': 'tool-use',\n  'Sparse outcome rewards reduce tool calls by 72%': 'tool-use',\n\n  // → reasoning\n  'test-time': 'reasoning',\n  'test-time-scaling': 'reasoning',\n  'inference-scaling': 'reasoning',\n  'inference-optimization': 'reasoning',\n  'self-critique': 'reasoning',\n  'self-reflection': 'reasoning',\n  'self-referential': 'reasoning',\n  'self-play': 'reasoning',\n  reflexion: 'reasoning',\n  reflection: 'reasoning',\n  'reasoning-optimization': 'reasoning',\n  'meta-thinking': 'reasoning',\n  scaling: 'reasoning',\n  recursive: 'reasoning',\n  'trajectory-abstraction': 'reasoning',\n  'verbal-rl': 'reasoning',\n  exploration: 'reasoning',\n  'Reducible uncertainty modeling across agent trajectories': 'reasoning',\n  'Environmental feedback reduces uncertainty at decision gates': 'reasoning',\n  'reinforcement-learning': 'reasoning',\n  transformer: 'reasoning',\n  ssm: 'reasoning',\n  'sparse-activation': 'reasoning',\n  'behavior-distillation': 'reasoning',\n  'training-free': 'reasoning',\n  'transfer-learning': 'reasoning',\n  'instruction-tuning': 'reasoning',\n  'Dense process rewards improve performance by 22%': 'reasoning',\n  'prompt-optimization': 'reasoning',\n};\n\n/**\n * Normalize a free-form topic string to a canonical topic.\n * Returns the canonical topic if a mapping exists, otherwise the original string.\n */\nexport function normalizeTopicToCanonical(topic: string): string {\n  return TOPIC_ALIASES[topic] ?? topic;\n}\n","/**\n * Research Synthesis Helper\n *\n * Groups papers by topic cluster and generates structured synthesis\n * summaries with themes, findings, and implementation opportunities.\n *\n * @module cli/research-helpers-synthesize\n * (Source: Issue #1386 — Research Synthesis Pipeline)\n */\n\nimport { loadPapersRegistry } from './research-helpers-io.js';\nimport type { PapersRegistry } from './research-types.js';\nimport type { Result } from '../core/result.js';\nimport { getErrorMessage } from '../core/index.js';\nimport { TECHNIQUE_IMPLEMENTATION_MAP, FEATURE_GATE_INVENTORY } from './research-alignment-map.js';\nimport { normalizeTopicToCanonical } from '../research/topic-aliases.js';\n\n// =============================================================================\n// TYPES\n// =============================================================================\n\n/** A paper entry from the registry, simplified for synthesis. */\nexport interface SynthesisPaper {\n  readonly id: string;\n  readonly title: string;\n  readonly topics: readonly string[];\n  readonly tags: readonly string[];\n  readonly summary: string;\n  readonly keyFindings: readonly string[];\n  readonly relevance: string;\n  readonly implementationStatus: string;\n  readonly techniquesExtracted: readonly string[];\n  readonly qualityScore: number;\n  readonly evidenceTier: 'high' | 'medium' | 'low';\n}\n\n/** A cluster of related papers grouped by topic. */\nexport interface PaperCluster {\n  readonly topic: string;\n  readonly papers: readonly SynthesisPaper[];\n  readonly paperCount: number;\n}\n\n/** A technique aligned to an existing implementation. */\nexport interface TechniqueAlignment {\n  readonly technique: string;\n  readonly status: 'implemented' | 'partial' | 'not-started';\n  readonly canonicalPath?: string | undefined;\n  readonly improvementHint?: string | undefined;\n}\n\n/** Quality distribution within a cluster. */\nexport interface QualityDistribution {\n  readonly avgScore: number;\n  readonly high: number;\n  readonly medium: number;\n  readonly low: number;\n}\n\n/** Synthesis output for a single topic cluster. */\nexport interface ClusterSynthesis {\n  readonly topic: string;\n  readonly paperCount: number;\n  readonly papers: readonly string[];\n  readonly commonThemes: readonly string[];\n  readonly keyInsights: readonly string[];\n  readonly techniques: readonly string[];\n  readonly implementationOpportunities: readonly string[];\n  readonly gaps: readonly string[];\n  readonly alignedTechniques: readonly TechniqueAlignment[];\n  readonly qualityDistribution: QualityDistribution;\n}\n\n/** Summary of alignment between research and implementation. */\nexport interface AlignmentSummary {\n  readonly implemented: number;\n  readonly partial: number;\n  readonly notStarted: number;\n  readonly total: number;\n  readonly topOpportunities: readonly string[];\n}\n\n/** Summary of a single feature gate for synthesis output. */\nexport interface FeatureGateStatus {\n  readonly envVar: string;\n  readonly defaultValue: string;\n  readonly description: string;\n  readonly linkedTechniqueCount: number;\n}\n\n/** Full synthesis result across all clusters. */\nexport interface SynthesisResult {\n  readonly clusters: readonly ClusterSynthesis[];\n  readonly totalPapers: number;\n  readonly topicCount: number;\n  readonly crossCuttingThemes: readonly string[];\n  readonly alignmentSummary: AlignmentSummary;\n  readonly featureGates: readonly FeatureGateStatus[];\n}\n\n/** Error for synthesis operations. */\nexport interface SynthesisError {\n  readonly code: 'LOAD_ERROR' | 'NO_PAPERS';\n  readonly message: string;\n}\n\n// =============================================================================\n// CONSTANTS\n// =============================================================================\n\n/** Minimum papers in a cluster to generate cross-cutting themes. */\nconst MIN_CROSS_CUTTING_CLUSTER_SIZE = 2;\n\n/** Tags that appear across many topics and indicate cross-cutting themes. */\nconst CROSS_CUTTING_TAG_THRESHOLD = 3;\n\n// =============================================================================\n// PUBLIC API\n// =============================================================================\n\n/**\n * Synthesize the research registry by grouping papers into topic clusters\n * and generating structured summaries.\n *\n * @param topicFilter - Optional topic to filter to a single cluster\n * @returns Structured synthesis result\n */\nexport async function synthesizeResearch(\n  topicFilter?: string\n): Promise<Result<SynthesisResult, SynthesisError>> {\n  const registryResult = await loadPapersRegistry();\n  if (!registryResult.ok) {\n    return {\n      ok: false,\n      error: {\n        code: 'LOAD_ERROR',\n        message: `Failed to load papers: ${getErrorMessage(registryResult.error)}`,\n      },\n    };\n  }\n\n  const papers = extractPapers(registryResult.value);\n  if (papers.length === 0) {\n    return {\n      ok: false,\n      error: { code: 'NO_PAPERS', message: 'No papers found in registry' },\n    };\n  }\n\n  const clusters = groupByTopic(papers);\n  const filtered =\n    topicFilter !== undefined ? clusters.filter((c) => c.topic === topicFilter) : clusters;\n\n  const syntheses = filtered.map(synthesizeCluster);\n  const crossCutting = findCrossCuttingThemes(filtered);\n  const alignmentSummary = buildAlignmentSummary(syntheses);\n  const featureGates = buildFeatureGateSummary();\n\n  return {\n    ok: true,\n    value: {\n      clusters: syntheses,\n      totalPapers: papers.length,\n      topicCount: filtered.length,\n      crossCuttingThemes: crossCutting,\n      alignmentSummary,\n      featureGates,\n    },\n  };\n}\n\n// =============================================================================\n// EXTRACTION\n// =============================================================================\n\n/**\n * Safely convert a field that types say is `readonly string[]` but may be\n * null/undefined at runtime (YAML parsing of empty array fields).\n */\nfunction safeArray(value: readonly string[]): string[] {\n  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition -- YAML parsing can yield null despite type\n  if (value === null || value === undefined) return [];\n  return Array.from(value);\n}\n\n/** Extract papers from the registry structure. */\nfunction extractPapers(registry: PapersRegistry): SynthesisPaper[] {\n  return Object.entries(registry.papers).map(([id, p]) => ({\n    id,\n    title: p.title,\n    topics: safeArray(p.topics),\n    tags: safeArray(p.tags),\n    summary: p.summary.trim(),\n    keyFindings: safeArray(p.key_findings),\n    relevance: p.relevance,\n    implementationStatus: p.implementation_status,\n    techniquesExtracted: safeArray(p.techniques_extracted),\n    qualityScore: p.quality_score ?? 0,\n    evidenceTier: p.evidence_tier ?? 'low',\n  }));\n}\n\n// =============================================================================\n// GROUPING\n// =============================================================================\n\n/** Group papers by primary topic into clusters, normalizing free-form topics. */\nfunction groupByTopic(papers: readonly SynthesisPaper[]): PaperCluster[] {\n  const topicMap = new Map<string, SynthesisPaper[]>();\n\n  for (const paper of papers) {\n    for (const rawTopic of paper.topics) {\n      const topic = normalizeTopicToCanonical(rawTopic);\n      const existing = topicMap.get(topic);\n      if (existing !== undefined) {\n        existing.push(paper);\n      } else {\n        topicMap.set(topic, [paper]);\n      }\n    }\n  }\n\n  const clusters: PaperCluster[] = [];\n  for (const [topic, unsortedPapers] of topicMap) {\n    // Sort papers within cluster by quality_score descending (high-quality first)\n    const topicPapers = [...unsortedPapers].sort((a, b) => b.qualityScore - a.qualityScore);\n    clusters.push({\n      topic,\n      papers: topicPapers,\n      paperCount: topicPapers.length,\n    });\n  }\n\n  return clusters.sort((a, b) => b.paperCount - a.paperCount);\n}\n\n// =============================================================================\n// SYNTHESIS\n// =============================================================================\n\n/** Generate synthesis for a single topic cluster. */\n/** Compute quality score distribution for a set of papers. */\nfunction computeClusterQuality(papers: readonly SynthesisPaper[]): QualityDistribution {\n  const scores = papers.map((p) => p.qualityScore);\n  const totalScore = scores.reduce((sum, s) => sum + s, 0);\n  return {\n    avgScore: scores.length > 0 ? Math.round((totalScore / scores.length) * 10) / 10 : 0,\n    high: papers.filter((p) => p.evidenceTier === 'high').length,\n    medium: papers.filter((p) => p.evidenceTier === 'medium').length,\n    low: papers.filter((p) => p.evidenceTier === 'low').length,\n  };\n}\n\nfunction synthesizeCluster(cluster: PaperCluster): ClusterSynthesis {\n  const allTags = collectFrequencies(cluster.papers.flatMap((p) => [...p.tags]));\n  const allTechniques = collectFrequencies(\n    cluster.papers.flatMap((p) => [...p.techniquesExtracted])\n  );\n  const allFindings = cluster.papers.flatMap((p) => [...p.keyFindings]);\n\n  // Common themes: tags that appear in 2+ papers\n  const commonThemes = [...allTags.entries()]\n    .filter(([, count]) => count >= MIN_CROSS_CUTTING_CLUSTER_SIZE)\n    .sort((a, b) => b[1] - a[1])\n    .map(([tag]) => tag);\n\n  // Techniques across the cluster\n  const techniques = [...allTechniques.entries()]\n    .sort((a, b) => b[1] - a[1])\n    .map(([tech, count]) => (count > 1 ? `${tech} (${String(count)} papers)` : tech));\n\n  // Implementation opportunities: techniques not yet implemented\n  const notStarted = cluster.papers\n    .filter((p) => p.implementationStatus === 'not-started')\n    .flatMap((p) => [...p.techniquesExtracted]);\n  const uniqueOpportunities = [...new Set(notStarted)];\n\n  // Gaps: topics with few papers or missing techniques\n  const gaps: string[] = [];\n  if (cluster.paperCount === 1) {\n    gaps.push(`Only 1 paper — more research needed on ${cluster.topic}`);\n  }\n  const highRelevanceUnimplemented = cluster.papers.filter(\n    (p) => p.relevance === 'high' && p.implementationStatus === 'not-started'\n  );\n  if (highRelevanceUnimplemented.length > 0) {\n    gaps.push(\n      `${String(highRelevanceUnimplemented.length)} high-relevance paper(s) not yet implemented`\n    );\n  }\n\n  // Alignment analysis: map techniques to existing implementations\n  const allTechNames = [...allTechniques.keys()];\n  const alignedTechniques = analyzeClusterAlignment(allTechNames);\n\n  const qualityDistribution = computeClusterQuality(cluster.papers);\n\n  // Add quality gap if most papers are low-quality\n  if (qualityDistribution.low > qualityDistribution.high + qualityDistribution.medium) {\n    gaps.push(\n      `Mostly low-evidence papers (${String(qualityDistribution.low)}/${String(cluster.paperCount)}) — findings need stronger validation`\n    );\n  }\n\n  return {\n    topic: cluster.topic,\n    paperCount: cluster.paperCount,\n    papers: cluster.papers.map((p) => p.title),\n    commonThemes,\n    keyInsights: deduplicateFindings(allFindings).slice(0, 10),\n    techniques,\n    implementationOpportunities: uniqueOpportunities,\n    gaps,\n    alignedTechniques,\n    qualityDistribution,\n  };\n}\n\n/** Find themes that span multiple topic clusters. */\nfunction findCrossCuttingThemes(clusters: readonly PaperCluster[]): string[] {\n  const tagToTopics = new Map<string, Set<string>>();\n\n  for (const cluster of clusters) {\n    for (const paper of cluster.papers) {\n      for (const tag of paper.tags) {\n        const existing = tagToTopics.get(tag);\n        if (existing !== undefined) {\n          existing.add(cluster.topic);\n        } else {\n          tagToTopics.set(tag, new Set([cluster.topic]));\n        }\n      }\n    }\n  }\n\n  return [...tagToTopics.entries()]\n    .filter(([, topics]) => topics.size >= CROSS_CUTTING_TAG_THRESHOLD)\n    .sort((a, b) => b[1].size - a[1].size)\n    .map(([tag, topics]) => `${tag} (spans: ${[...topics].join(', ')})`);\n}\n\n// =============================================================================\n// ALIGNMENT ANALYSIS\n// =============================================================================\n\n/** Analyze technique alignment for a cluster. */\nfunction analyzeClusterAlignment(techniques: readonly string[]): TechniqueAlignment[] {\n  const alignments: TechniqueAlignment[] = [];\n\n  for (const tech of techniques) {\n    // Strip count annotation like \"technique (2 papers)\"\n    const baseTech = tech.replace(/\\s*\\(\\d+\\s*papers?\\)$/, '');\n    const mapping = TECHNIQUE_IMPLEMENTATION_MAP.get(baseTech);\n\n    if (mapping !== undefined) {\n      alignments.push({\n        technique: baseTech,\n        status: mapping.status,\n        canonicalPath: mapping.path,\n        ...(mapping.hint !== undefined ? { improvementHint: mapping.hint } : {}),\n      });\n    } else {\n      alignments.push({ technique: baseTech, status: 'not-started' });\n    }\n  }\n\n  return alignments;\n}\n\n/** Build alignment summary across all clusters. */\nfunction buildAlignmentSummary(clusters: readonly ClusterSynthesis[]): AlignmentSummary {\n  const allAlignments = clusters.flatMap((c) => c.alignedTechniques);\n  const implemented = allAlignments.filter((a) => a.status === 'implemented').length;\n  const partial = allAlignments.filter((a) => a.status === 'partial').length;\n  const notStarted = allAlignments.filter((a) => a.status === 'not-started').length;\n\n  // Top opportunities: partial implementations with hints (most improvable)\n  const opportunities = allAlignments\n    .filter((a) => a.status === 'partial' && a.improvementHint !== undefined)\n    .map((a) => `${a.technique}: ${a.improvementHint ?? ''}`)\n    .slice(0, 10);\n\n  return {\n    implemented,\n    partial,\n    notStarted,\n    total: allAlignments.length,\n    topOpportunities: opportunities,\n  };\n}\n\n/** Build feature gate summary from the inventory. */\nfunction buildFeatureGateSummary(): FeatureGateStatus[] {\n  return FEATURE_GATE_INVENTORY.map((g) => ({\n    envVar: g.envVar,\n    defaultValue: g.defaultValue,\n    description: g.description,\n    linkedTechniqueCount: g.techniques?.length ?? 0,\n  }));\n}\n\n// =============================================================================\n// UTILITIES\n// =============================================================================\n\nfunction collectFrequencies(items: readonly string[]): Map<string, number> {\n  const counts = new Map<string, number>();\n  for (const item of items) {\n    counts.set(item, (counts.get(item) ?? 0) + 1);\n  }\n  return counts;\n}\n\n/** Deduplicate findings by removing near-identical strings. */\nfunction deduplicateFindings(findings: readonly string[]): string[] {\n  const seen = new Set<string>();\n  const result: string[] = [];\n  for (const finding of findings) {\n    const normalized = finding.toLowerCase().trim();\n    if (normalized.length === 0) continue;\n    if (seen.has(normalized)) continue;\n    seen.add(normalized);\n    result.push(finding);\n  }\n  return 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