CHECKPOINT: Brainy 2.0 API refactor - pre-fixes state

Current state:
- Unified augmentation system to BrainyAugmentation interface
- Changed methods to specific noun/verb naming (addNoun, getNoun, etc)
- Made old methods private
- Combined getNouns into single unified method
- Neural API exists and is complete
- Triple Intelligence uses correct Brainy operators (not MongoDB)

Issues identified:
- Documentation incorrectly shows MongoDB operators (code is correct)
- Need to ensure all features are properly exposed
- Need to verify nothing was lost in simplification

This commit serves as a rollback point before applying fixes.

src/index.ts

@@ -0,0 +1,502 @@
+/**
+ * Brainy - Your AI-Powered Second Brain
+ * 🧠⚛️ A multi-dimensional database with vector, graph, and facet storage
+ * 
+ * Core Components:
+ * - BrainyData: The brain (core database)
+ * - Cortex: The orchestrator (manages augmentations)
+ * - NeuralImport: AI-powered data understanding
+ * - Augmentations: Brain capabilities (plugins)
+ */
+
+// Export main BrainyData class and related types
+import { BrainyData, BrainyDataConfig } from './brainyData.js'
+
+export { BrainyData }
+export type { BrainyDataConfig }
+
+// Export Cortex (the orchestrator)
+export { 
+  Cortex, 
+  cortex
+} from './cortex.js'
+
+// Export Neural Import (AI data understanding)
+export { NeuralImport } from './cortex/neuralImport.js'
+export type { 
+  NeuralAnalysisResult,
+  DetectedEntity,
+  DetectedRelationship,
+  NeuralInsight,
+  NeuralImportOptions 
+} from './cortex/neuralImport.js'
+
+// Augmentation types are already exported later in the file
+
+// Export distance functions for convenience
+import {
+  euclideanDistance,
+  cosineDistance,
+  manhattanDistance,
+  dotProductDistance,
+  getStatistics
+} from './utils/index.js'
+
+export {
+  euclideanDistance,
+  cosineDistance,
+  manhattanDistance,
+  dotProductDistance,
+  getStatistics
+}
+
+// Export embedding functionality
+import {
+  UniversalSentenceEncoder,
+  TransformerEmbedding,
+  createEmbeddingFunction,
+  defaultEmbeddingFunction,
+  batchEmbed,
+  embeddingFunctions
+} from './utils/embedding.js'
+
+// Export worker utilities
+import { executeInThread, cleanupWorkerPools } from './utils/workerUtils.js'
+
+// Export logging utilities
+import { 
+  logger, 
+  LogLevel, 
+  configureLogger, 
+  createModuleLogger 
+} from './utils/logger.js'
+
+// Export BrainyChat for conversational AI
+import { BrainyChat } from './chat/BrainyChat.js'
+export { BrainyChat }
+
+// Export Cortex CLI functionality - commented out for core MIT build
+// export { Cortex } from './cortex/cortex.js'
+
+// Export performance and optimization utilities
+import {
+  getGlobalSocketManager,
+  AdaptiveSocketManager
+} from './utils/adaptiveSocketManager.js'
+
+import {
+  getGlobalBackpressure,
+  AdaptiveBackpressure
+} from './utils/adaptiveBackpressure.js'
+
+import {
+  getGlobalPerformanceMonitor,
+  PerformanceMonitor
+} from './utils/performanceMonitor.js'
+
+// Export environment utilities
+import {
+  isBrowser,
+  isNode,
+  isWebWorker,
+  areWebWorkersAvailable,
+  areWorkerThreadsAvailable,
+  areWorkerThreadsAvailableSync,
+  isThreadingAvailable,
+  isThreadingAvailableAsync
+} from './utils/environment.js'
+
+export {
+  UniversalSentenceEncoder,
+  TransformerEmbedding,
+  createEmbeddingFunction,
+  defaultEmbeddingFunction,
+  batchEmbed,
+  embeddingFunctions,
+
+  // Worker utilities
+  executeInThread,
+  cleanupWorkerPools,
+
+  // Environment utilities
+  isBrowser,
+  isNode,
+  isWebWorker,
+  areWebWorkersAvailable,
+  areWorkerThreadsAvailable,
+  areWorkerThreadsAvailableSync,
+  isThreadingAvailable,
+  isThreadingAvailableAsync,
+  
+  // Logging utilities
+  logger,
+  LogLevel,
+  configureLogger,
+  createModuleLogger,
+  
+  // Performance and optimization utilities
+  getGlobalSocketManager,
+  AdaptiveSocketManager,
+  getGlobalBackpressure,
+  AdaptiveBackpressure,
+  getGlobalPerformanceMonitor,
+  PerformanceMonitor
+}
+
+// Export storage adapters
+import {
+  OPFSStorage,
+  MemoryStorage,
+  R2Storage,
+  S3CompatibleStorage,
+  createStorage
+} from './storage/storageFactory.js'
+
+export {
+  OPFSStorage,
+  MemoryStorage,
+  R2Storage,
+  S3CompatibleStorage,
+  createStorage
+}
+
+// FileSystemStorage is exported separately to avoid browser build issues
+export { FileSystemStorage } from './storage/adapters/fileSystemStorage.js'
+
+// Export unified pipeline
+import {
+  Pipeline,
+  pipeline,
+  augmentationPipeline,
+  ExecutionMode,
+  PipelineOptions,
+  PipelineResult,
+  createPipeline,
+  createStreamingPipeline,
+  StreamlinedExecutionMode,
+  StreamlinedPipelineOptions,
+  StreamlinedPipelineResult
+} from './pipeline.js'
+
+// Sequential pipeline removed - use unified pipeline instead
+
+// Export augmentation factory
+import {
+  createSenseAugmentation,
+  addWebSocketSupport,
+  executeAugmentation,
+  loadAugmentationModule,
+  AugmentationOptions
+} from './augmentationFactory.js'
+
+export {
+  // Unified pipeline exports
+  Pipeline,
+  pipeline,
+  augmentationPipeline,
+  ExecutionMode,
+
+  // Factory functions
+  createPipeline,
+  createStreamingPipeline,
+  StreamlinedExecutionMode,
+
+  // Augmentation factory exports
+  createSenseAugmentation,
+  addWebSocketSupport,
+  executeAugmentation,
+  loadAugmentationModule
+}
+export type {
+  PipelineOptions,
+  PipelineResult,
+  StreamlinedPipelineOptions,
+  StreamlinedPipelineResult,
+  AugmentationOptions
+}
+
+// Export augmentation registry for build-time loading
+import {
+  availableAugmentations,
+  registerAugmentation,
+  initializeAugmentationPipeline,
+  setAugmentationEnabled,
+  getAugmentationsByType
+} from './augmentationRegistry.js'
+
+export {
+  availableAugmentations,
+  registerAugmentation,
+  initializeAugmentationPipeline,
+  setAugmentationEnabled,
+  getAugmentationsByType
+}
+
+// Export augmentation registry loader for build tools
+import {
+  loadAugmentationsFromModules,
+  createAugmentationRegistryPlugin,
+  createAugmentationRegistryRollupPlugin
+} from './augmentationRegistryLoader.js'
+import type {
+  AugmentationRegistryLoaderOptions,
+  AugmentationLoadResult
+} from './augmentationRegistryLoader.js'
+
+export {
+  loadAugmentationsFromModules,
+  createAugmentationRegistryPlugin,
+  createAugmentationRegistryRollupPlugin
+}
+export type { AugmentationRegistryLoaderOptions, AugmentationLoadResult }
+
+
+// Export augmentation implementations
+import {
+  StorageAugmentation,
+  DynamicStorageAugmentation,
+  createStorageAugmentationFromConfig
+} from './augmentations/storageAugmentation.js'
+import {
+  MemoryStorageAugmentation,
+  FileSystemStorageAugmentation,
+  OPFSStorageAugmentation,
+  S3StorageAugmentation,
+  R2StorageAugmentation,
+  GCSStorageAugmentation,
+  createAutoStorageAugmentation
+} from './augmentations/storageAugmentations.js'
+import {
+  WebSocketConduitAugmentation,
+  WebRTCConduitAugmentation,
+  createConduitAugmentation
+} from './augmentations/conduitAugmentations.js'
+import {
+  ServerSearchConduitAugmentation,
+  ServerSearchActivationAugmentation,
+  createServerSearchAugmentations
+} from './augmentations/serverSearchAugmentations.js'
+
+// Storage augmentation exports
+export {
+  // Base classes
+  StorageAugmentation,
+  DynamicStorageAugmentation,
+  // Concrete implementations
+  MemoryStorageAugmentation,
+  FileSystemStorageAugmentation,
+  OPFSStorageAugmentation,
+  S3StorageAugmentation,
+  R2StorageAugmentation,
+  GCSStorageAugmentation,
+  // Factory functions
+  createAutoStorageAugmentation,
+  createStorageAugmentationFromConfig
+}
+
+// Other augmentation exports
+export {
+  WebSocketConduitAugmentation,
+  ServerSearchConduitAugmentation,
+  ServerSearchActivationAugmentation,
+  createServerSearchAugmentations
+}
+
+// LLM augmentations are optional and not imported by default
+// They can be imported directly from their module if needed:
+// import { LLMCognitionAugmentation, LLMActivationAugmentation, createLLMAugmentations } from './augmentations/llmAugmentations.js'
+
+// Export types
+import type {
+  Vector,
+  VectorDocument,
+  SearchResult,
+  DistanceFunction,
+  EmbeddingFunction,
+  EmbeddingModel,
+  HNSWNoun,
+  HNSWVerb,
+  HNSWConfig,
+  StorageAdapter
+} from './coreTypes.js'
+
+// Export HNSW index and optimized version
+import { HNSWIndex } from './hnsw/hnswIndex.js'
+import {
+  HNSWIndexOptimized,
+  HNSWOptimizedConfig
+} from './hnsw/hnswIndexOptimized.js'
+
+export { HNSWIndex, HNSWIndexOptimized }
+
+export type {
+  Vector,
+  VectorDocument,
+  SearchResult,
+  DistanceFunction,
+  EmbeddingFunction,
+  EmbeddingModel,
+  HNSWNoun,
+  HNSWVerb,
+  HNSWConfig,
+  HNSWOptimizedConfig,
+  StorageAdapter
+}
+
+// Export augmentation types
+import type {
+  IAugmentation,
+  AugmentationResponse,
+  IWebSocketSupport,
+  ISenseAugmentation,
+  IConduitAugmentation,
+  ICognitionAugmentation,
+  IMemoryAugmentation,
+  IPerceptionAugmentation,
+  IDialogAugmentation,
+  IActivationAugmentation
+} from './types/augmentations.js'
+import { AugmentationType, BrainyAugmentations } from './types/augmentations.js'
+
+// Export augmentation manager for type-safe augmentation management
+export { AugmentationManager, type AugmentationInfo } from './augmentationManager.js'
+
+export type { IAugmentation, AugmentationResponse, IWebSocketSupport }
+export {
+  AugmentationType,
+  BrainyAugmentations,
+  ISenseAugmentation,
+  IConduitAugmentation,
+  ICognitionAugmentation,
+  IMemoryAugmentation,
+  IPerceptionAugmentation,
+  IDialogAugmentation,
+  IActivationAugmentation
+}
+
+// Export combined WebSocket augmentation interfaces
+export type {
+  IWebSocketCognitionAugmentation,
+  IWebSocketSenseAugmentation,
+  IWebSocketPerceptionAugmentation,
+  IWebSocketActivationAugmentation,
+  IWebSocketDialogAugmentation,
+  IWebSocketConduitAugmentation,
+  IWebSocketMemoryAugmentation
+} from './types/augmentations.js'
+
+// Export graph types
+import type {
+  GraphNoun,
+  GraphVerb,
+  EmbeddedGraphVerb,
+  Person,
+  Location,
+  Thing,
+  Event,
+  Concept,
+  Content,
+  Collection,
+  Organization,
+  Document,
+  Media,
+  File,
+  Message,
+  Dataset,
+  Product,
+  Service,
+  User,
+  Task,
+  Project,
+  Process,
+  State,
+  Role,
+  Topic,
+  Language,
+  Currency,
+  Measurement
+} from './types/graphTypes.js'
+import { NounType, VerbType } from './types/graphTypes.js'
+
+export type {
+  GraphNoun,
+  GraphVerb,
+  EmbeddedGraphVerb,
+  Person,
+  Location,
+  Thing,
+  Event,
+  Concept,
+  Content,
+  Collection,
+  Organization,
+  Document,
+  Media,
+  File,
+  Message,
+  Dataset,
+  Product,
+  Service,
+  User,
+  Task,
+  Project,
+  Process,
+  State,
+  Role,
+  Topic,
+  Language,
+  Currency,
+  Measurement
+}
+// Export type utility functions
+import { getNounTypes, getVerbTypes, getNounTypeMap, getVerbTypeMap } from './utils/typeUtils.js'
+
+export { 
+  NounType, 
+  VerbType,
+  getNounTypes,
+  getVerbTypes,
+  getNounTypeMap,
+  getVerbTypeMap
+}
+
+// Export MCP (Model Control Protocol) components
+import {
+  BrainyMCPAdapter,
+  MCPAugmentationToolset,
+  BrainyMCPService
+} from './mcp/index.js' // Import from mcp/index.js
+import {
+  MCPRequest,
+  MCPResponse,
+  MCPDataAccessRequest,
+  MCPToolExecutionRequest,
+  MCPSystemInfoRequest,
+  MCPAuthenticationRequest,
+  MCPRequestType,
+  MCPServiceOptions,
+  MCPTool,
+  MCP_VERSION
+} from './types/mcpTypes.js'
+
+export {
+  // MCP classes
+  BrainyMCPAdapter,
+  MCPAugmentationToolset,
+  BrainyMCPService,
+
+  // MCP types
+  MCPRequestType,
+  MCP_VERSION
+}
+
+export type {
+  MCPRequest,
+  MCPResponse,
+  MCPDataAccessRequest,
+  MCPToolExecutionRequest,
+  MCPSystemInfoRequest,
+  MCPAuthenticationRequest,
+  MCPServiceOptions,
+  MCPTool
+}