chore: recovery checkpoint - v3.0 API successfully recovered

CRITICAL CHECKPOINT - DO NOT PUSH TO GITHUB

Recovery Status:
- Successfully recovered brainy.ts from compiled JavaScript
- All core v3.0 API methods functional (add, get, update, delete, relate, find, etc.)
- Neural subsystem intact (562KB embedded patterns, NLP working)
- Augmentation pipeline operational (20+ augmentations)
- HNSW clustering system complete
- Triple Intelligence compiled (needs constructor fix)
- Test suite validates functionality

Changes preserved:
- 898 files with changes from last 3 days
- 144,475 insertions
- All augmentation improvements
- All test coverage enhancements
- Complete v3.0 feature set

This is a LOCAL checkpoint only - contains recovered work after corruption incident.
Created backup in .backups/brainy-full-20250910-151314.tar.gz

Branch: recovery-checkpoint-20250910-151433
Date: Wed Sep 10 03:18:04 PM PDT 2025

.recovery-workspace/dist-backup-20250910-141917/index.js

@@ -0,0 +1,124 @@
+/**
+ * Brainy 3.0 - Your AI-Powered Second Brain
+ * 🧠⚛️ A multi-dimensional database with vector, graph, and relational storage
+ *
+ * Core Components:
+ * - Brainy: The unified database with Triple Intelligence
+ * - Triple Intelligence: Seamless fusion of vector + graph + field search
+ * - Augmentations: Extensible plugin system
+ * - Neural API: AI-powered clustering and analysis
+ */
+// Export main Brainy class - the modern, clean API for Brainy 3.0
+import { Brainy } from './brainy.js';
+export { Brainy };
+// Export zero-configuration types and enums
+export { 
+// Preset names
+PresetName, 
+// Model configuration
+ModelPrecision, 
+// Storage configuration  
+StorageOption, 
+// Feature configuration
+FeatureSet, 
+// Distributed roles
+DistributedRole, 
+// Categories
+PresetCategory, registerStorageAugmentation, registerPresetAugmentation, 
+// Preset utilities
+getPreset, isValidPreset, getPresetsByCategory, getAllPresetNames, getPresetDescription } from './config/index.js';
+// Export Cortex (the orchestrator)
+export { Cortex, cortex } from './cortex.js';
+// Export Neural Import (AI data understanding)
+export { NeuralImport } from './cortex/neuralImport.js';
+// Augmentation types are already exported later in the file
+// Export distance functions for convenience
+import { euclideanDistance, cosineDistance, manhattanDistance, dotProductDistance } from './utils/index.js';
+export { euclideanDistance, cosineDistance, manhattanDistance, dotProductDistance };
+// Export version utilities
+export { getBrainyVersion } from './utils/version.js';
+// 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';
+// Chat system removed - was returning fake responses
+// 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, createPipeline, createStreamingPipeline, StreamlinedExecutionMode } from './pipeline.js';
+// Sequential pipeline removed - use unified pipeline instead
+// REMOVED: Old augmentation factory for 2.0 clean architecture
+export { 
+// Unified pipeline exports
+Pipeline, pipeline, augmentationPipeline, ExecutionMode, 
+// Factory functions
+createPipeline, createStreamingPipeline, StreamlinedExecutionMode,
+// Augmentation factory exports (REMOVED in 2.0 - Use BrainyAugmentation interface)
+// createSenseAugmentation,     // → Use BaseAugmentation class
+// addWebSocketSupport,         // → Use APIServerAugmentation  
+// executeAugmentation,         // → Use brain.augmentations.execute()
+// loadAugmentationModule       // → Use dynamic imports
+ };
+// Augmentation registry removed - use Brainy's built-in augmentation system
+// Export augmentation registry loader for build tools
+import { loadAugmentationsFromModules, createAugmentationRegistryPlugin, createAugmentationRegistryRollupPlugin } from './augmentationRegistryLoader.js';
+export { loadAugmentationsFromModules, createAugmentationRegistryPlugin, createAugmentationRegistryRollupPlugin };
+// 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 } from './augmentations/conduitAugmentations.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 };
+// Export HNSW index and optimized version
+import { HNSWIndex } from './hnsw/hnswIndex.js';
+import { HNSWIndexOptimized } from './hnsw/hnswIndexOptimized.js';
+export { HNSWIndex, HNSWIndexOptimized };
+// Export augmentation manager for type-safe augmentation management
+export { AugmentationManager } from './augmentationManager.js';
+import { NounType, VerbType } from './types/graphTypes.js';
+// Export type utility functions
+import { getNounTypes, getVerbTypes, getNounTypeMap, getVerbTypeMap } from './utils/typeUtils.js';
+// Export BrainyTypes for complete type management
+import { BrainyTypes, suggestType } from './utils/brainyTypes.js';
+export { NounType, VerbType, getNounTypes, getVerbTypes, getNounTypeMap, getVerbTypeMap, 
+// BrainyTypes - complete type management
+BrainyTypes, suggestType };
+// Export MCP (Model Control Protocol) components
+import { BrainyMCPAdapter, MCPAugmentationToolset, BrainyMCPService } from './mcp/index.js'; // Import from mcp/index.js
+import { MCPRequestType, MCP_VERSION } from './types/mcpTypes.js';
+export { 
+// MCP classes
+BrainyMCPAdapter, MCPAugmentationToolset, BrainyMCPService, 
+// MCP types
+MCPRequestType, MCP_VERSION };
+//# sourceMappingURL=index.js.map