raggrep 0.1.0

package/dist/cli/main.js.map

@@ -0,0 +1,22 @@
+{
+  "version": 3,
+  "sources": ["../../src/utils/embeddings.ts", "../../src/domain/entities/config.ts", "../../src/domain/entities/index.ts", "../../src/utils/config.ts", "../../src/domain/services/bm25.ts", "../../src/modules/semantic/parseCode.ts", "../../src/domain/services/keywords.ts", "../../src/utils/tieredIndex.ts", "../../src/modules/semantic/index.ts", "../../src/modules/registry.ts", "../../src/indexer/index.ts", "../../src/search/index.ts", "../../src/cli/main.ts"],
+  "sourcesContent": [
+    "// Local embedding provider using Transformers.js\n// Models are automatically downloaded and cached on first use\n\nimport { pipeline, env, type FeatureExtractionPipeline } from '@xenova/transformers';\nimport * as path from 'path';\nimport * as os from 'os';\n\n// ============================================================================\n// Configuration\n// ============================================================================\n\n// Configure cache directory for models\n// Uses ~/.cache/raggrep/models by default\nconst CACHE_DIR = path.join(os.homedir(), '.cache', 'raggrep', 'models');\n\n// Set the cache directory for transformers.js\nenv.cacheDir = CACHE_DIR;\n\n// Disable local model check (always try to use cache first, then download)\nenv.allowLocalModels = true;\n\n// Available embedding models (smaller = faster, larger = better quality)\nexport const EMBEDDING_MODELS = {\n  // Default: Good balance of speed and quality (~33M params, 384 dimensions)\n  'all-MiniLM-L6-v2': 'Xenova/all-MiniLM-L6-v2',\n  \n  // Higher quality, slightly slower (~33M params, 384 dimensions)\n  'all-MiniLM-L12-v2': 'Xenova/all-MiniLM-L12-v2',\n  \n  // BGE small - good for code (~33M params, 384 dimensions)\n  'bge-small-en-v1.5': 'Xenova/bge-small-en-v1.5',\n  \n  // Even smaller/faster option (~22M params, 384 dimensions)\n  'paraphrase-MiniLM-L3-v2': 'Xenova/paraphrase-MiniLM-L3-v2',\n} as const;\n\nexport type EmbeddingModelName = keyof typeof EMBEDDING_MODELS;\n\n// ============================================================================\n// Embedding Provider\n// ============================================================================\n\nlet embeddingPipeline: FeatureExtractionPipeline | null = null;\nlet currentModelName: string | null = null;\nlet isInitializing = false;\nlet initPromise: Promise<void> | null = null;\n\nexport interface EmbeddingConfig {\n  model: EmbeddingModelName;\n  /** Show progress during model download */\n  showProgress?: boolean;\n}\n\nconst DEFAULT_CONFIG: EmbeddingConfig = {\n  model: 'all-MiniLM-L6-v2',\n  showProgress: true,\n};\n\nlet currentConfig: EmbeddingConfig = { ...DEFAULT_CONFIG };\n\n/**\n * Configure the embedding model\n */\nexport function configureEmbeddings(config: Partial<EmbeddingConfig>): void {\n  const newConfig = { ...currentConfig, ...config };\n  \n  // If model changed, reset pipeline\n  if (newConfig.model !== currentConfig.model) {\n    embeddingPipeline = null;\n    currentModelName = null;\n  }\n  \n  currentConfig = newConfig;\n}\n\n/**\n * Initialize the embedding pipeline (downloads model if needed)\n */\nasync function initializePipeline(): Promise<void> {\n  if (embeddingPipeline && currentModelName === currentConfig.model) {\n    return;\n  }\n  \n  // Prevent multiple simultaneous initializations\n  if (isInitializing && initPromise) {\n    return initPromise;\n  }\n  \n  isInitializing = true;\n  \n  initPromise = (async () => {\n    const modelId = EMBEDDING_MODELS[currentConfig.model];\n    \n    if (currentConfig.showProgress) {\n      console.log(`\\n  Loading embedding model: ${currentConfig.model}`);\n      console.log(`  Cache: ${CACHE_DIR}`);\n    }\n    \n    try {\n      // Create the feature extraction pipeline\n      // This will download the model on first run\n      embeddingPipeline = await pipeline('feature-extraction', modelId, {\n        progress_callback: currentConfig.showProgress \n          ? (progress: { status: string; file?: string; progress?: number; loaded?: number; total?: number }) => {\n              if (progress.status === 'progress' && progress.file) {\n                const pct = progress.progress ? Math.round(progress.progress) : 0;\n                process.stdout.write(`\\r  Downloading ${progress.file}: ${pct}%   `);\n              } else if (progress.status === 'done' && progress.file) {\n                process.stdout.write(`\\r  Downloaded ${progress.file}              \\n`);\n              } else if (progress.status === 'ready') {\n                // Model is ready\n              }\n            }\n          : undefined,\n      });\n      \n      currentModelName = currentConfig.model;\n      \n      if (currentConfig.showProgress) {\n        console.log(`  Model ready.\\n`);\n      }\n    } catch (error) {\n      embeddingPipeline = null;\n      currentModelName = null;\n      throw new Error(`Failed to load embedding model: ${error}`);\n    } finally {\n      isInitializing = false;\n      initPromise = null;\n    }\n  })();\n  \n  return initPromise;\n}\n\n/**\n * Get embedding for a single text\n */\nexport async function getEmbedding(text: string): Promise<number[]> {\n  await initializePipeline();\n  \n  if (!embeddingPipeline) {\n    throw new Error('Embedding pipeline not initialized');\n  }\n  \n  // Get embeddings using mean pooling\n  const output = await embeddingPipeline(text, {\n    pooling: 'mean',\n    normalize: true,\n  });\n  \n  // Convert to array\n  return Array.from(output.data as Float32Array);\n}\n\n/** Maximum number of texts to process in a single batch */\nconst BATCH_SIZE = 32;\n\n/**\n * Get embeddings for multiple texts (batched for efficiency)\n * \n * Processes texts in batches of BATCH_SIZE for better performance\n * while avoiding memory issues with very large batches.\n * \n * @param texts - Array of texts to embed\n * @returns Array of embedding vectors\n */\nexport async function getEmbeddings(texts: string[]): Promise<number[][]> {\n  if (texts.length === 0) return [];\n  \n  await initializePipeline();\n  \n  if (!embeddingPipeline) {\n    throw new Error('Embedding pipeline not initialized');\n  }\n  \n  const results: number[][] = [];\n  \n  // Process in batches for efficiency\n  for (let i = 0; i < texts.length; i += BATCH_SIZE) {\n    const batch = texts.slice(i, i + BATCH_SIZE);\n    \n    // Process batch - transformers.js handles array inputs\n    const outputs = await Promise.all(\n      batch.map(async (text) => {\n        const output = await embeddingPipeline!(text, {\n          pooling: 'mean',\n          normalize: true,\n        });\n        return Array.from(output.data as Float32Array);\n      })\n    );\n    \n    results.push(...outputs);\n  }\n  \n  return results;\n}\n\n// ============================================================================\n// Vector Math\n// ============================================================================\n\n/**\n * Calculate cosine similarity between two vectors\n */\nexport function cosineSimilarity(a: number[], b: number[]): number {\n  if (a.length !== b.length) {\n    throw new Error('Vectors must have the same length');\n  }\n\n  let dotProduct = 0;\n  let normA = 0;\n  let normB = 0;\n\n  for (let i = 0; i < a.length; i++) {\n    dotProduct += a[i] * b[i];\n    normA += a[i] * a[i];\n    normB += b[i] * b[i];\n  }\n\n  if (normA === 0 || normB === 0) return 0;\n\n  return dotProduct / (Math.sqrt(normA) * Math.sqrt(normB));\n}\n\n/**\n * Get current embedding configuration\n */\nexport function getEmbeddingConfig(): EmbeddingConfig {\n  return { ...currentConfig };\n}\n\n/**\n * Get the cache directory path\n */\nexport function getCacheDir(): string {\n  return CACHE_DIR;\n}\n\n/**\n * Check if a model is already cached\n */\nexport async function isModelCached(model: EmbeddingModelName = currentConfig.model): Promise<boolean> {\n  const modelId = EMBEDDING_MODELS[model];\n  const modelPath = path.join(CACHE_DIR, modelId.replace('/', '--'));\n  \n  try {\n    const fs = await import('fs/promises');\n    await fs.access(modelPath);\n    return true;\n  } catch {\n    return false;\n  }\n}\n",
+    "/**\n * Config Entity\n * \n * Configuration for RAGgrep indexing and search operations.\n */\n\n/**\n * Configuration for a specific index module.\n */\nexport interface ModuleConfig {\n  /** Unique module identifier */\n  id: string;\n  \n  /** Whether the module is enabled */\n  enabled: boolean;\n  \n  /** Module-specific options */\n  options?: Record<string, unknown>;\n}\n\n/**\n * Main RAGgrep configuration.\n */\nexport interface Config {\n  /** RAGgrep version */\n  version: string;\n  \n  /** Directory name for index storage (default: '.raggrep') */\n  indexDir: string;\n  \n  /** File extensions to index (e.g., ['.ts', '.tsx', '.js']) */\n  extensions: string[];\n  \n  /** Paths to ignore during indexing */\n  ignorePaths: string[];\n  \n  /** Enabled modules and their configurations */\n  modules: ModuleConfig[];\n}\n\n/**\n * Default paths to ignore during indexing.\n */\nexport const DEFAULT_IGNORE_PATHS = [\n  // Package managers & dependencies\n  'node_modules',\n  '.pnpm-store',\n  '.yarn',\n  'vendor',\n  \n  // Version control\n  '.git',\n  \n  // Build outputs\n  'dist',\n  'build',\n  'out',\n  '.output',\n  'target',\n  \n  // Framework-specific build outputs\n  '.next',\n  '.nuxt',\n  '.svelte-kit',\n  '.vercel',\n  '.netlify',\n  \n  // Caches\n  '.cache',\n  '.turbo',\n  '.parcel-cache',\n  '.eslintcache',\n  \n  // Test & coverage\n  'coverage',\n  '.nyc_output',\n  \n  // Python\n  '__pycache__',\n  '.venv',\n  'venv',\n  '.pytest_cache',\n  '*.egg-info',\n  \n  // IDE & editor\n  '.idea',\n  \n  // RAGgrep index\n  '.raggrep',\n];\n\n/**\n * Default file extensions to index.\n */\nexport const DEFAULT_EXTENSIONS = [\n  '.ts', '.tsx', '.js', '.jsx',\n  '.py', '.go', '.rs', '.java', '.md',\n];\n\n/**\n * Create a default configuration.\n */\nexport function createDefaultConfig(): Config {\n  return {\n    version: '0.1.0',\n    indexDir: '.raggrep',\n    extensions: DEFAULT_EXTENSIONS,\n    ignorePaths: DEFAULT_IGNORE_PATHS,\n    modules: [\n      {\n        id: 'semantic',\n        enabled: true,\n        options: {\n          embeddingModel: 'all-MiniLM-L6-v2',\n        },\n      },\n    ],\n  };\n}\n\n",
+    "/**\n * Domain Entities\n *\n * Core business objects with no external dependencies.\n * These represent the fundamental concepts in the RAGgrep domain.\n */\n\n// Chunk - The fundamental unit of indexing\nexport type { Chunk, ChunkType } from \"./chunk\";\nexport { createChunkId } from \"./chunk\";\n\n// FileIndex - Tier 2 full index data\nexport type {\n  FileIndex,\n  FileManifestEntry,\n  ModuleManifest,\n  GlobalManifest,\n} from \"./fileIndex\";\n\n// FileSummary - Symbolic index (lightweight summaries)\nexport type {\n  FileSummary,\n  SymbolicIndexMeta,\n  Tier1Manifest,\n} from \"./fileSummary\";\n\n// SearchResult - Query results\nexport type { SearchResult, SearchOptions } from \"./searchResult\";\nexport { DEFAULT_SEARCH_OPTIONS } from \"./searchResult\";\n\n// Config - Application configuration\nexport type { Config, ModuleConfig } from \"./config\";\nexport {\n  DEFAULT_IGNORE_PATHS,\n  DEFAULT_EXTENSIONS,\n  createDefaultConfig,\n} from \"./config\";\n",
+    "/**\n * Configuration utilities\n * \n * Provides functions for loading, saving, and managing RAGgrep configuration.\n */\n\nimport * as path from 'path';\nimport * as fs from 'fs/promises';\nimport type { Config, ModuleConfig } from '../domain/entities';\nimport { createDefaultConfig } from '../domain/entities';\nimport { EmbeddingConfig, EmbeddingModelName, EMBEDDING_MODELS } from './embeddings';\n\n/** Default configuration instance */\nexport const DEFAULT_CONFIG: Config = createDefaultConfig();\n\n/**\n * Get the root .raggrep directory path\n */\nexport function getRaggrepDir(rootDir: string, config: Config = DEFAULT_CONFIG): string {\n  return path.join(rootDir, config.indexDir);\n}\n\n/**\n * Get the index data directory for a specific module\n */\nexport function getModuleIndexPath(rootDir: string, moduleId: string, config: Config = DEFAULT_CONFIG): string {\n  return path.join(rootDir, config.indexDir, 'index', moduleId);\n}\n\n/**\n * Get the manifest path for a specific module\n */\nexport function getModuleManifestPath(rootDir: string, moduleId: string, config: Config = DEFAULT_CONFIG): string {\n  return path.join(rootDir, config.indexDir, 'index', moduleId, 'manifest.json');\n}\n\n/**\n * Get the global manifest path\n */\nexport function getGlobalManifestPath(rootDir: string, config: Config = DEFAULT_CONFIG): string {\n  return path.join(rootDir, config.indexDir, 'manifest.json');\n}\n\n/**\n * Get the config file path\n */\nexport function getConfigPath(rootDir: string, config: Config = DEFAULT_CONFIG): string {\n  return path.join(rootDir, config.indexDir, 'config.json');\n}\n\n/**\n * Load config from file or return default\n */\nexport async function loadConfig(rootDir: string): Promise<Config> {\n  const configPath = getConfigPath(rootDir, DEFAULT_CONFIG);\n  \n  try {\n    const content = await fs.readFile(configPath, 'utf-8');\n    const savedConfig = JSON.parse(content) as Partial<Config>;\n    return { ...DEFAULT_CONFIG, ...savedConfig };\n  } catch {\n    return DEFAULT_CONFIG;\n  }\n}\n\n/**\n * Save config to file\n */\nexport async function saveConfig(rootDir: string, config: Config): Promise<void> {\n  const configPath = getConfigPath(rootDir, config);\n  await fs.mkdir(path.dirname(configPath), { recursive: true });\n  await fs.writeFile(configPath, JSON.stringify(config, null, 2));\n}\n\n/**\n * Get module config by ID\n */\nexport function getModuleConfig(config: Config, moduleId: string): ModuleConfig | undefined {\n  return config.modules.find(m => m.id === moduleId);\n}\n\n/**\n * Extract embedding config from module options\n */\nexport function getEmbeddingConfigFromModule(moduleConfig: ModuleConfig): EmbeddingConfig {\n  const options = moduleConfig.options || {};\n  const modelName = (options.embeddingModel as string) || 'all-MiniLM-L6-v2';\n  \n  // Validate model name\n  if (!(modelName in EMBEDDING_MODELS)) {\n    console.warn(`Unknown embedding model: ${modelName}, falling back to all-MiniLM-L6-v2`);\n    return { model: 'all-MiniLM-L6-v2' };\n  }\n  \n  return {\n    model: modelName as EmbeddingModelName,\n    showProgress: options.showProgress !== false,\n  };\n}\n",
+    "/**\n * BM25 (Best Matching 25) Implementation\n * \n * A ranking function for keyword-based search. This is a pure domain service\n * with no external dependencies - just algorithms operating on data.\n * \n * BM25 estimates relevance of documents to a search query using term frequency\n * and inverse document frequency with length normalization.\n */\n\n/**\n * BM25 parameters\n * - k1: Term frequency saturation (typical: 1.2-2.0)\n * - b: Length normalization (typical: 0.75)\n */\nconst BM25_K1 = 1.5;\nconst BM25_B = 0.75;\n\n/**\n * Tokenize text into normalized terms.\n * \n * @param text - Text to tokenize\n * @returns Array of lowercase tokens\n */\nexport function tokenize(text: string): string[] {\n  return text\n    .toLowerCase()\n    .replace(/[^\\w\\s]/g, ' ')\n    .split(/\\s+/)\n    .filter(token => token.length > 1);\n}\n\n/**\n * Calculate term frequency (TF) for a term in a document.\n */\nfunction termFrequency(term: string, tokens: string[]): number {\n  return tokens.filter(t => t === term).length;\n}\n\n/**\n * Document data for BM25 scoring.\n */\nexport interface BM25Document {\n  id: string;\n  content: string;\n  /** Pre-computed tokens (optional, computed from content if not provided) */\n  tokens?: string[];\n}\n\n/**\n * BM25 search result.\n */\nexport interface BM25Result {\n  id: string;\n  score: number;\n}\n\n/**\n * BM25 search index.\n * \n * This is a pure in-memory data structure with no I/O operations.\n * Build the index by adding documents, then search against it.\n */\nexport class BM25Index {\n  private documents: Map<string, { content: string; tokens: string[] }> = new Map();\n  private avgDocLength: number = 0;\n  private documentFrequencies: Map<string, number> = new Map();\n  private totalDocs: number = 0;\n\n  /**\n   * Add documents to the index.\n   * \n   * @param documents - Array of documents to index\n   */\n  addDocuments(documents: BM25Document[]): void {\n    let totalLength = this.avgDocLength * this.totalDocs;\n\n    for (const doc of documents) {\n      const tokens = doc.tokens ?? tokenize(doc.content);\n      this.documents.set(doc.id, { content: doc.content, tokens });\n      totalLength += tokens.length;\n      this.totalDocs++;\n\n      // Update document frequencies\n      const uniqueTerms = new Set(tokens);\n      for (const term of uniqueTerms) {\n        const count = this.documentFrequencies.get(term) || 0;\n        this.documentFrequencies.set(term, count + 1);\n      }\n    }\n\n    this.avgDocLength = this.totalDocs > 0 ? totalLength / this.totalDocs : 0;\n  }\n\n  /**\n   * Calculate IDF (Inverse Document Frequency) for a term.\n   */\n  private idf(term: string): number {\n    const docFreq = this.documentFrequencies.get(term) || 0;\n    if (docFreq === 0) return 0;\n    \n    // Standard IDF formula with smoothing\n    return Math.log(1 + (this.totalDocs - docFreq + 0.5) / (docFreq + 0.5));\n  }\n\n  /**\n   * Calculate BM25 score for a document given query terms.\n   */\n  private score(tokens: string[], queryTerms: string[]): number {\n    const docLength = tokens.length;\n    let score = 0;\n\n    for (const term of queryTerms) {\n      const tf = termFrequency(term, tokens);\n      if (tf === 0) continue;\n\n      const idfScore = this.idf(term);\n      \n      // BM25 formula\n      const numerator = tf * (BM25_K1 + 1);\n      const denominator = tf + BM25_K1 * (1 - BM25_B + BM25_B * (docLength / this.avgDocLength));\n      \n      score += idfScore * (numerator / denominator);\n    }\n\n    return score;\n  }\n\n  /**\n   * Search the index with a query.\n   * \n   * @param query - Search query\n   * @param topK - Maximum number of results to return\n   * @returns Sorted array of results (highest score first)\n   */\n  search(query: string, topK: number = 10): BM25Result[] {\n    const queryTerms = tokenize(query);\n    if (queryTerms.length === 0) return [];\n\n    const results: BM25Result[] = [];\n\n    for (const [id, { tokens }] of this.documents) {\n      const score = this.score(tokens, queryTerms);\n      if (score > 0) {\n        results.push({ id, score });\n      }\n    }\n\n    results.sort((a, b) => b.score - a.score);\n    return results.slice(0, topK);\n  }\n\n  /**\n   * Get the number of indexed documents.\n   */\n  get size(): number {\n    return this.totalDocs;\n  }\n\n  /**\n   * Clear the index.\n   */\n  clear(): void {\n    this.documents.clear();\n    this.documentFrequencies.clear();\n    this.avgDocLength = 0;\n    this.totalDocs = 0;\n  }\n}\n\n/**\n * Normalize a raw score to 0-1 range using sigmoid function.\n * \n * @param score - Raw score\n * @param midpoint - Score at which output is 0.5\n * @returns Normalized score between 0 and 1\n */\nexport function normalizeScore(score: number, midpoint: number = 5): number {\n  return 1 / (1 + Math.exp(-score / midpoint + 1));\n}\n\n",
+    "/**\n * TypeScript/JavaScript Code Parser\n * \n * Uses the TypeScript Compiler API for accurate AST-based parsing.\n * Extracts semantic chunks: functions, classes, interfaces, types, enums.\n */\n\nimport * as ts from 'typescript';\n\n/**\n * Chunk types that can be extracted from code\n */\nexport type ChunkType = \n  | 'function' \n  | 'class' \n  | 'interface' \n  | 'type' \n  | 'enum'\n  | 'variable'\n  | 'block' \n  | 'file';\n\n/**\n * Represents a parsed chunk of code with location information\n */\nexport interface ParsedChunk {\n  /** The source code content */\n  content: string;\n  /** 1-based start line number */\n  startLine: number;\n  /** 1-based end line number */\n  endLine: number;\n  /** The type of code construct */\n  type: ChunkType;\n  /** Name of the construct (function name, class name, etc.) */\n  name?: string;\n  /** Whether this is exported */\n  isExported?: boolean;\n  /** JSDoc comment if present */\n  jsDoc?: string;\n}\n\n/**\n * Parse code into semantic chunks based on file extension\n * @param content - The source code content\n * @param filepath - The file path (used to determine language)\n * @returns Array of parsed chunks\n */\nexport function parseCode(content: string, filepath: string): ParsedChunk[] {\n  const ext = filepath.split('.').pop()?.toLowerCase();\n\n  // For TypeScript/JavaScript files, use the TypeScript parser\n  if (['ts', 'tsx', 'js', 'jsx', 'mts', 'cts', 'mjs', 'cjs'].includes(ext || '')) {\n    return parseTypeScript(content, filepath);\n  }\n\n  // For other files, use simple line-based chunking\n  return parseGenericCode(content);\n}\n\n/**\n * Parse TypeScript/JavaScript code using the TypeScript Compiler API\n * @param content - The source code content\n * @param filepath - The file path\n * @returns Array of parsed chunks\n */\nfunction parseTypeScript(content: string, filepath: string): ParsedChunk[] {\n  const chunks: ParsedChunk[] = [];\n  const lines = content.split('\\n');\n\n  // Create a source file from the content\n  const sourceFile = ts.createSourceFile(\n    filepath,\n    content,\n    ts.ScriptTarget.Latest,\n    true, // setParentNodes\n    filepath.endsWith('.tsx') || filepath.endsWith('.jsx') \n      ? ts.ScriptKind.TSX \n      : ts.ScriptKind.TS\n  );\n\n  /**\n   * Get line numbers for a node (1-based)\n   */\n  function getLineNumbers(node: ts.Node): { startLine: number; endLine: number } {\n    const start = sourceFile.getLineAndCharacterOfPosition(node.getStart());\n    const end = sourceFile.getLineAndCharacterOfPosition(node.getEnd());\n    return {\n      startLine: start.line + 1,\n      endLine: end.line + 1,\n    };\n  }\n\n  /**\n   * Get the source text for a node\n   */\n  function getNodeText(node: ts.Node): string {\n    return node.getText(sourceFile);\n  }\n\n  /**\n   * Check if a node has export modifier\n   */\n  function isExported(node: ts.Node): boolean {\n    if (!ts.canHaveModifiers(node)) return false;\n    const modifiers = ts.getModifiers(node);\n    return modifiers?.some(m => m.kind === ts.SyntaxKind.ExportKeyword) ?? false;\n  }\n\n  /**\n   * Get JSDoc comment for a node\n   */\n  function getJSDoc(node: ts.Node): string | undefined {\n    const jsDocNodes = ts.getJSDocCommentsAndTags(node);\n    if (jsDocNodes.length === 0) return undefined;\n    \n    return jsDocNodes\n      .map(doc => doc.getText(sourceFile))\n      .join('\\n');\n  }\n\n  /**\n   * Get function name from various function declarations\n   */\n  function getFunctionName(node: ts.Node): string | undefined {\n    if (ts.isFunctionDeclaration(node) && node.name) {\n      return node.name.text;\n    }\n    if (ts.isMethodDeclaration(node) && ts.isIdentifier(node.name)) {\n      return node.name.text;\n    }\n    if (ts.isVariableDeclaration(node) && ts.isIdentifier(node.name)) {\n      return node.name.text;\n    }\n    return undefined;\n  }\n\n  /**\n   * Visit nodes recursively to extract chunks\n   */\n  function visit(node: ts.Node): void {\n    const { startLine, endLine } = getLineNumbers(node);\n\n    // Function declarations (including async)\n    if (ts.isFunctionDeclaration(node) && node.name) {\n      chunks.push({\n        content: getNodeText(node),\n        startLine,\n        endLine,\n        type: 'function',\n        name: node.name.text,\n        isExported: isExported(node),\n        jsDoc: getJSDoc(node),\n      });\n      return; // Don't recurse into function body\n    }\n\n    // Arrow functions and function expressions assigned to variables\n    if (ts.isVariableStatement(node)) {\n      for (const decl of node.declarationList.declarations) {\n        if (decl.initializer && \n            (ts.isArrowFunction(decl.initializer) || ts.isFunctionExpression(decl.initializer))) {\n          const name = ts.isIdentifier(decl.name) ? decl.name.text : undefined;\n          chunks.push({\n            content: getNodeText(node),\n            startLine,\n            endLine,\n            type: 'function',\n            name,\n            isExported: isExported(node),\n            jsDoc: getJSDoc(node),\n          });\n          return;\n        }\n      }\n    }\n\n    // Class declarations\n    if (ts.isClassDeclaration(node) && node.name) {\n      chunks.push({\n        content: getNodeText(node),\n        startLine,\n        endLine,\n        type: 'class',\n        name: node.name.text,\n        isExported: isExported(node),\n        jsDoc: getJSDoc(node),\n      });\n      return; // Don't recurse into class body (it's included in the chunk)\n    }\n\n    // Interface declarations\n    if (ts.isInterfaceDeclaration(node)) {\n      chunks.push({\n        content: getNodeText(node),\n        startLine,\n        endLine,\n        type: 'interface',\n        name: node.name.text,\n        isExported: isExported(node),\n        jsDoc: getJSDoc(node),\n      });\n      return;\n    }\n\n    // Type alias declarations\n    if (ts.isTypeAliasDeclaration(node)) {\n      chunks.push({\n        content: getNodeText(node),\n        startLine,\n        endLine,\n        type: 'type',\n        name: node.name.text,\n        isExported: isExported(node),\n        jsDoc: getJSDoc(node),\n      });\n      return;\n    }\n\n    // Enum declarations\n    if (ts.isEnumDeclaration(node)) {\n      chunks.push({\n        content: getNodeText(node),\n        startLine,\n        endLine,\n        type: 'enum',\n        name: node.name.text,\n        isExported: isExported(node),\n        jsDoc: getJSDoc(node),\n      });\n      return;\n    }\n\n    // Exported variable declarations (constants)\n    if (ts.isVariableStatement(node) && isExported(node)) {\n      for (const decl of node.declarationList.declarations) {\n        // Skip if it's a function (already handled above)\n        if (decl.initializer && \n            (ts.isArrowFunction(decl.initializer) || ts.isFunctionExpression(decl.initializer))) {\n          continue;\n        }\n        const name = ts.isIdentifier(decl.name) ? decl.name.text : undefined;\n        chunks.push({\n          content: getNodeText(node),\n          startLine,\n          endLine,\n          type: 'variable',\n          name,\n          isExported: true,\n          jsDoc: getJSDoc(node),\n        });\n      }\n      return;\n    }\n\n    // Recurse into children\n    ts.forEachChild(node, visit);\n  }\n\n  // Start visiting from the root\n  ts.forEachChild(sourceFile, visit);\n\n  // If no semantic chunks found, fall back to block-based chunking\n  if (chunks.length === 0) {\n    return parseGenericCode(content);\n  }\n\n  return chunks;\n}\n\n/**\n * Parse generic code using line-based chunking\n * Used for non-TypeScript/JavaScript files or as fallback\n * @param content - The source code content\n * @returns Array of parsed chunks\n */\nfunction parseGenericCode(content: string): ParsedChunk[] {\n  const chunks: ParsedChunk[] = [];\n  const lines = content.split('\\n');\n  const CHUNK_SIZE = 30; // lines per chunk\n  const OVERLAP = 5; // overlap between chunks\n\n  // If file is small, treat as single chunk\n  if (lines.length <= CHUNK_SIZE) {\n    return [\n      {\n        content: content,\n        startLine: 1,\n        endLine: lines.length,\n        type: 'file',\n      },\n    ];\n  }\n\n  // Split into overlapping chunks\n  for (let i = 0; i < lines.length; i += CHUNK_SIZE - OVERLAP) {\n    const endIdx = Math.min(i + CHUNK_SIZE, lines.length);\n    chunks.push({\n      content: lines.slice(i, endIdx).join('\\n'),\n      startLine: i + 1,\n      endLine: endIdx,\n      type: 'block',\n    });\n\n    if (endIdx >= lines.length) break;\n  }\n\n  return chunks;\n}\n\n/**\n * Generate a unique chunk ID from filepath and line numbers\n * @param filepath - The source file path\n * @param startLine - Start line number\n * @param endLine - End line number\n * @returns Unique chunk identifier\n */\nexport function generateChunkId(filepath: string, startLine: number, endLine: number): string {\n  const safePath = filepath.replace(/[/\\\\]/g, '-').replace(/\\./g, '_');\n  return `${safePath}-${startLine}-${endLine}`;\n}\n",
+    "/**\n * Keyword Extraction Service\n * \n * Pure domain service for extracting keywords from code.\n * No external dependencies - operates only on string data.\n */\n\n/**\n * Common programming keywords to exclude from keyword extraction.\n * These appear in almost every code file and don't add search value.\n */\nexport const COMMON_KEYWORDS = new Set([\n  // JavaScript/TypeScript\n  'const', 'let', 'var', 'function', 'class', 'interface', 'type', 'enum',\n  'export', 'import', 'from', 'return', 'async', 'await', 'new', 'this',\n  'true', 'false', 'null', 'undefined', 'if', 'else', 'for', 'while',\n  'switch', 'case', 'break', 'continue', 'try', 'catch', 'finally',\n  'throw', 'typeof', 'instanceof', 'void', 'delete', 'in', 'of',\n  'string', 'number', 'boolean', 'any', 'unknown', 'never', 'object',\n  'public', 'private', 'protected', 'static', 'readonly', 'abstract',\n  'implements', 'extends', 'super', 'get', 'set', 'constructor',\n  // Common words\n  'the', 'and', 'for', 'not', 'with', 'are', 'was', 'has', 'have',\n]);\n\n/**\n * Extract keywords from code content and optional name.\n * \n * @param content - Code content to extract keywords from\n * @param name - Optional name (function name, class name, etc.)\n * @param maxKeywords - Maximum keywords to return (default: 50)\n * @returns Array of unique lowercase keywords\n */\nexport function extractKeywords(\n  content: string, \n  name?: string,\n  maxKeywords: number = 50\n): string[] {\n  const keywords = new Set<string>();\n  \n  // Add the name if present\n  if (name) {\n    keywords.add(name.toLowerCase());\n    \n    // Also add camelCase parts (e.g., \"getUserById\" → [\"get\", \"user\", \"by\", \"id\"])\n    const parts = name.split(/(?=[A-Z])/).map(p => p.toLowerCase());\n    parts.forEach(p => p.length > 2 && keywords.add(p));\n  }\n  \n  // Extract identifiers from content\n  const identifierRegex = /\\b([a-zA-Z_][a-zA-Z0-9_]{2,})\\b/g;\n  let match;\n  \n  while ((match = identifierRegex.exec(content)) !== null) {\n    const word = match[1].toLowerCase();\n    \n    // Skip common keywords and very short words\n    if (!COMMON_KEYWORDS.has(word) && word.length > 2) {\n      keywords.add(word);\n    }\n  }\n  \n  return Array.from(keywords).slice(0, maxKeywords);\n}\n\n/**\n * Extract keywords from a file path.\n * \n * @param filepath - File path to extract keywords from\n * @returns Array of keywords from path segments\n */\nexport function extractPathKeywords(filepath: string): string[] {\n  return filepath\n    .split(/[/\\\\.]/)\n    .filter(p => p.length > 2 && !COMMON_KEYWORDS.has(p.toLowerCase()))\n    .map(p => p.toLowerCase());\n}\n\n",
+    "/**\n * Symbolic Index System\n * \n * Provides fast keyword-based filtering using BM25 before semantic search.\n * \n * Structure:\n *   .raggrep/index/<module>/symbolic/\n *   ├── _meta.json    (BM25 statistics)\n *   └── <filepath>.json (per-file summaries)\n * \n * This approach scales well because:\n * - Each file summary is stored separately\n * - BM25 metadata is small and loads quickly\n * - Summaries are loaded on-demand during search\n */\n\nimport * as fs from 'fs/promises';\nimport * as path from 'path';\nimport { BM25Index } from '../domain/services/bm25';\nimport { extractKeywords, extractPathKeywords } from '../domain/services/keywords';\nimport type { FileSummary, SymbolicIndexMeta } from '../domain/entities';\n\n// Re-export for backwards compatibility\nexport type { FileSummary, SymbolicIndexMeta } from '../domain/entities';\nexport { extractKeywords } from '../domain/services/keywords';\n\n/** @deprecated Use SymbolicIndexMeta */\nexport type Tier1Manifest = SymbolicIndexMeta & { files: Record<string, FileSummary> };\n\n/**\n * Symbolic Index Manager\n * \n * Manages the keyword-based index for fast file filtering.\n */\nexport class SymbolicIndex {\n  private meta: SymbolicIndexMeta | null = null;\n  private fileSummaries: Map<string, FileSummary> = new Map();\n  private bm25Index: BM25Index | null = null;\n  private symbolicPath: string;\n  private moduleId: string;\n\n  constructor(indexDir: string, moduleId: string) {\n    this.symbolicPath = path.join(indexDir, 'index', moduleId, 'symbolic');\n    this.moduleId = moduleId;\n  }\n\n  /**\n   * Initialize or load the symbolic index\n   */\n  async initialize(): Promise<void> {\n    try {\n      await this.load();\n    } catch {\n      // Create empty metadata\n      this.meta = {\n        version: '1.0.0',\n        lastUpdated: new Date().toISOString(),\n        moduleId: this.moduleId,\n        fileCount: 0,\n        bm25Data: {\n          avgDocLength: 0,\n          documentFrequencies: {},\n          totalDocs: 0,\n        },\n      };\n      this.bm25Index = new BM25Index();\n    }\n  }\n\n  /**\n   * Add or update a file summary\n   */\n  addFile(summary: FileSummary): void {\n    this.fileSummaries.set(summary.filepath, summary);\n  }\n\n  /**\n   * Remove a file from the index\n   */\n  removeFile(filepath: string): boolean {\n    return this.fileSummaries.delete(filepath);\n  }\n\n  /**\n   * Build BM25 index from file summaries\n   */\n  buildBM25Index(): void {\n    this.bm25Index = new BM25Index();\n    \n    // Add each file's keywords as a document\n    for (const [filepath, summary] of this.fileSummaries) {\n      const content = [\n        ...summary.keywords,\n        ...summary.exports,\n        ...extractPathKeywords(filepath),\n      ].join(' ');\n      \n      this.bm25Index.addDocuments([{ id: filepath, content }]);\n    }\n    \n    // Update metadata\n    if (this.meta) {\n      this.meta.fileCount = this.fileSummaries.size;\n      this.meta.bm25Data.totalDocs = this.fileSummaries.size;\n    }\n  }\n\n  /**\n   * Find candidate files using BM25 keyword search\n   */\n  findCandidates(query: string, maxCandidates: number = 20): string[] {\n    if (!this.bm25Index) {\n      return Array.from(this.fileSummaries.keys());\n    }\n    \n    const results = this.bm25Index.search(query, maxCandidates);\n    return results.map(r => r.id);\n  }\n\n  /**\n   * Get all file paths in the index\n   */\n  getAllFiles(): string[] {\n    return Array.from(this.fileSummaries.keys());\n  }\n\n  /**\n   * Get summary for a specific file\n   */\n  getFileSummary(filepath: string): FileSummary | undefined {\n    return this.fileSummaries.get(filepath);\n  }\n\n  /**\n   * Save the index to disk (per-file structure)\n   */\n  async save(): Promise<void> {\n    if (!this.meta) throw new Error('Index not initialized');\n    \n    // Update metadata\n    this.meta.lastUpdated = new Date().toISOString();\n    this.meta.fileCount = this.fileSummaries.size;\n    \n    // Ensure symbolic directory exists\n    await fs.mkdir(this.symbolicPath, { recursive: true });\n    \n    // Save metadata\n    const metaPath = path.join(this.symbolicPath, '_meta.json');\n    await fs.writeFile(metaPath, JSON.stringify(this.meta, null, 2));\n    \n    // Save each file summary\n    for (const [filepath, summary] of this.fileSummaries) {\n      const summaryPath = this.getFileSummaryPath(filepath);\n      await fs.mkdir(path.dirname(summaryPath), { recursive: true });\n      await fs.writeFile(summaryPath, JSON.stringify(summary, null, 2));\n    }\n  }\n\n  /**\n   * Load the index from disk\n   */\n  async load(): Promise<void> {\n    // Load metadata\n    const metaPath = path.join(this.symbolicPath, '_meta.json');\n    const metaContent = await fs.readFile(metaPath, 'utf-8');\n    this.meta = JSON.parse(metaContent);\n    \n    // Load all file summaries by walking the symbolic directory\n    this.fileSummaries.clear();\n    await this.loadFileSummariesRecursive(this.symbolicPath);\n    \n    // Rebuild BM25 index\n    this.buildBM25Index();\n  }\n\n  /**\n   * Recursively load file summaries from the symbolic directory\n   */\n  private async loadFileSummariesRecursive(dir: string): Promise<void> {\n    try {\n      const entries = await fs.readdir(dir, { withFileTypes: true });\n      \n      for (const entry of entries) {\n        const fullPath = path.join(dir, entry.name);\n        \n        if (entry.isDirectory()) {\n          await this.loadFileSummariesRecursive(fullPath);\n        } else if (entry.name.endsWith('.json') && entry.name !== '_meta.json') {\n          try {\n            const content = await fs.readFile(fullPath, 'utf-8');\n            const summary = JSON.parse(content) as FileSummary;\n            if (summary.filepath) {\n              this.fileSummaries.set(summary.filepath, summary);\n            }\n          } catch {\n            // Skip invalid files\n          }\n        }\n      }\n    } catch {\n      // Directory doesn't exist yet\n    }\n  }\n\n  /**\n   * Get the path for a file summary\n   */\n  private getFileSummaryPath(filepath: string): string {\n    const jsonPath = filepath.replace(/\\.[^.]+$/, '.json');\n    return path.join(this.symbolicPath, jsonPath);\n  }\n\n  /**\n   * Delete a file summary from disk\n   */\n  async deleteFileSummary(filepath: string): Promise<void> {\n    try {\n      await fs.unlink(this.getFileSummaryPath(filepath));\n    } catch {\n      // Ignore if file doesn't exist\n    }\n    this.fileSummaries.delete(filepath);\n  }\n\n  /**\n   * Check if the index exists on disk\n   */\n  async exists(): Promise<boolean> {\n    try {\n      const metaPath = path.join(this.symbolicPath, '_meta.json');\n      await fs.access(metaPath);\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Get the number of indexed files\n   */\n  get size(): number {\n    return this.fileSummaries.size;\n  }\n\n  /**\n   * Clear the index\n   */\n  clear(): void {\n    this.fileSummaries.clear();\n    if (this.meta) {\n      this.meta.fileCount = 0;\n      this.meta.bm25Data = {\n        avgDocLength: 0,\n        documentFrequencies: {},\n        totalDocs: 0,\n      };\n    }\n    this.bm25Index = new BM25Index();\n  }\n}\n\n// ============================================================================\n// Backwards compatibility aliases\n// ============================================================================\n\n/** @deprecated Use SymbolicIndex instead */\nexport const Tier1Index = SymbolicIndex;\n\n/** @deprecated Use SymbolicIndex instead */\nexport function getTier1Path(rootDir: string, moduleId: string, indexDir: string = '.raggrep'): string {\n  return path.join(rootDir, indexDir, 'index', moduleId, 'tier1.json');\n}\n\nexport function getSymbolicPath(rootDir: string, moduleId: string, indexDir: string = '.raggrep'): string {\n  return path.join(rootDir, indexDir, 'index', moduleId, 'symbolic');\n}\n",
+    "/**\n * Semantic Index Module\n * \n * Uses local text embeddings for natural language code search.\n * Implements a tiered index system:\n * - Tier 1: Lightweight file summaries with keywords for fast filtering\n * - Tier 2: Full chunk embeddings for semantic similarity\n * \n * This approach keeps the filesystem-based design while enabling\n * efficient search by only loading relevant files.\n */\n\nimport * as path from 'path';\nimport {\n  IndexModule,\n  IndexContext,\n  SearchContext,\n  SearchOptions,\n  FileIndex,\n  SearchResult,\n  Chunk,\n  ModuleConfig,\n  ChunkType,\n} from '../../types';\nimport {\n  getEmbeddings,\n  getEmbedding,\n  cosineSimilarity,\n  configureEmbeddings,\n  EmbeddingConfig,\n  getEmbeddingConfig,\n} from '../../utils/embeddings';\nimport { BM25Index, normalizeScore } from '../../utils/bm25';\nimport { getEmbeddingConfigFromModule, getRaggrepDir } from '../../utils/config';\nimport { parseCode, generateChunkId } from './parseCode';\nimport { SymbolicIndex, FileSummary, extractKeywords } from '../../utils/tieredIndex';\n\n/** Default minimum similarity score for search results */\nexport const DEFAULT_MIN_SCORE = 0.15;\n\n/** Default number of results to return */\nexport const DEFAULT_TOP_K = 10;\n\n/** Weight for semantic similarity in hybrid scoring (0-1) */\nconst SEMANTIC_WEIGHT = 0.7;\n\n/** Weight for BM25 keyword matching in hybrid scoring (0-1) */\nconst BM25_WEIGHT = 0.3;\n\n/**\n * Module-specific data stored alongside file index\n */\nexport interface SemanticModuleData {\n  embeddings: number[][];\n  /** Store the model used for these embeddings for compatibility checking */\n  embeddingModel: string;\n  [key: string]: unknown; // Index signature for compatibility with Record<string, unknown>\n}\n\n/** Number of candidate files to retrieve from Tier 1 before loading Tier 2 */\nconst TIER1_CANDIDATE_MULTIPLIER = 3;\n\nexport class SemanticModule implements IndexModule {\n  readonly id = 'semantic';\n  readonly name = 'Semantic Search';\n  readonly description = 'Natural language code search using local text embeddings';\n  readonly version = '1.0.0';\n\n  private embeddingConfig: EmbeddingConfig | null = null;\n  private symbolicIndex: SymbolicIndex | null = null;\n  private pendingSummaries: Map<string, FileSummary> = new Map();\n  private rootDir: string = '';\n\n  async initialize(config: ModuleConfig): Promise<void> {\n    // Extract embedding config from module options\n    this.embeddingConfig = getEmbeddingConfigFromModule(config);\n    \n    // Configure the embedding provider\n    configureEmbeddings(this.embeddingConfig);\n    \n    // Clear pending summaries for fresh indexing\n    this.pendingSummaries.clear();\n  }\n\n  async indexFile(\n    filepath: string,\n    content: string,\n    ctx: IndexContext\n  ): Promise<FileIndex | null> {\n    // Store rootDir for finalize\n    this.rootDir = ctx.rootDir;\n    \n    // Parse code into chunks\n    const parsedChunks = parseCode(content, filepath);\n\n    if (parsedChunks.length === 0) {\n      return null;\n    }\n\n    // Generate embeddings for all chunks\n    const chunkContents = parsedChunks.map((c) => c.content);\n    const embeddings = await getEmbeddings(chunkContents);\n\n    // Create chunks with all metadata\n    const chunks: Chunk[] = parsedChunks.map((pc) => ({\n      id: generateChunkId(filepath, pc.startLine, pc.endLine),\n      content: pc.content,\n      startLine: pc.startLine,\n      endLine: pc.endLine,\n      type: pc.type,\n      name: pc.name,\n      isExported: pc.isExported,\n      jsDoc: pc.jsDoc,\n    }));\n\n    // Extract references (imports)\n    const references = this.extractReferences(content, filepath);\n\n    const stats = await ctx.getFileStats(filepath);\n    const currentConfig = getEmbeddingConfig();\n\n    const moduleData: SemanticModuleData = {\n      embeddings,\n      embeddingModel: currentConfig.model,\n    };\n\n    // Build Tier 1 summary for this file\n    const chunkTypes = [...new Set(parsedChunks.map(pc => pc.type))] as ChunkType[];\n    const exports = parsedChunks\n      .filter(pc => pc.isExported && pc.name)\n      .map(pc => pc.name!);\n    \n    // Extract keywords from all chunks\n    const allKeywords = new Set<string>();\n    for (const pc of parsedChunks) {\n      const keywords = extractKeywords(pc.content, pc.name);\n      keywords.forEach(k => allKeywords.add(k));\n    }\n\n    const fileSummary: FileSummary = {\n      filepath,\n      chunkCount: chunks.length,\n      chunkTypes,\n      keywords: Array.from(allKeywords),\n      exports,\n      lastModified: stats.lastModified,\n    };\n    \n    // Store summary for finalize\n    this.pendingSummaries.set(filepath, fileSummary);\n\n    return {\n      filepath,\n      lastModified: stats.lastModified,\n      chunks,\n      moduleData,\n      references,\n    };\n  }\n\n  /**\n   * Finalize indexing by building and saving the symbolic index\n   */\n  async finalize(ctx: IndexContext): Promise<void> {\n    const indexDir = getRaggrepDir(ctx.rootDir, ctx.config);\n    \n    // Initialize symbolic index\n    this.symbolicIndex = new SymbolicIndex(indexDir, this.id);\n    await this.symbolicIndex.initialize();\n    \n    // Add all pending summaries\n    for (const [filepath, summary] of this.pendingSummaries) {\n      this.symbolicIndex.addFile(summary);\n    }\n    \n    // Build BM25 index from summaries\n    this.symbolicIndex.buildBM25Index();\n    \n    // Save to disk (creates symbolic/ folder with per-file summaries)\n    await this.symbolicIndex.save();\n    \n    console.log(`  Symbolic index built with ${this.pendingSummaries.size} file summaries`);\n    \n    // Clear pending summaries\n    this.pendingSummaries.clear();\n  }\n\n  /**\n   * Search the semantic index for chunks matching the query.\n   * \n   * Uses a tiered approach for efficient search:\n   * 1. Tier 1: Use BM25 on file summaries to find candidate files\n   * 2. Tier 2: Load only candidate files and compute semantic similarity\n   * \n   * @param query - Natural language search query\n   * @param ctx - Search context with index access\n   * @param options - Search options (topK, minScore, filePatterns)\n   * @returns Array of search results sorted by relevance\n   */\n  async search(\n    query: string,\n    ctx: SearchContext,\n    options: SearchOptions = {}\n  ): Promise<SearchResult[]> {\n    const { topK = DEFAULT_TOP_K, minScore = DEFAULT_MIN_SCORE, filePatterns } = options;\n\n    // Load symbolic index for candidate filtering\n    const indexDir = getRaggrepDir(ctx.rootDir, ctx.config);\n    const symbolicIndex = new SymbolicIndex(indexDir, this.id);\n    \n    let candidateFiles: string[];\n    \n    try {\n      await symbolicIndex.initialize();\n      \n      // Use BM25 keyword search on symbolic index to find candidate files\n      const maxCandidates = topK * TIER1_CANDIDATE_MULTIPLIER;\n      candidateFiles = symbolicIndex.findCandidates(query, maxCandidates);\n      \n      // If no candidates found via BM25, fall back to all files\n      if (candidateFiles.length === 0) {\n        candidateFiles = symbolicIndex.getAllFiles();\n      }\n    } catch {\n      // Symbolic index doesn't exist, fall back to loading all files\n      candidateFiles = await ctx.listIndexedFiles();\n    }\n\n    // Apply file pattern filter\n    if (filePatterns && filePatterns.length > 0) {\n      candidateFiles = candidateFiles.filter(filepath => {\n        return filePatterns.some(pattern => {\n          if (pattern.startsWith('*.')) {\n            const ext = pattern.slice(1);\n            return filepath.endsWith(ext);\n          }\n          return filepath.includes(pattern);\n        });\n      });\n    }\n\n    // Get query embedding for semantic search\n    const queryEmbedding = await getEmbedding(query);\n\n    // Tier 2: Load only candidate files and compute scores\n    const bm25Index = new BM25Index();\n    const allChunksData: Array<{\n      filepath: string;\n      chunk: Chunk;\n      embedding: number[];\n    }> = [];\n\n    for (const filepath of candidateFiles) {\n      const fileIndex = await ctx.loadFileIndex(filepath);\n      if (!fileIndex) continue;\n\n      const moduleData = fileIndex.moduleData as unknown as SemanticModuleData;\n      if (!moduleData?.embeddings) continue;\n\n      for (let i = 0; i < fileIndex.chunks.length; i++) {\n        const chunk = fileIndex.chunks[i];\n        const embedding = moduleData.embeddings[i];\n\n        if (!embedding) continue;\n\n        allChunksData.push({\n          filepath: fileIndex.filepath,\n          chunk,\n          embedding,\n        });\n\n        // Add to BM25 index for chunk-level keyword matching\n        bm25Index.addDocuments([{ id: chunk.id, content: chunk.content }]);\n      }\n    }\n\n    // Perform BM25 search at chunk level\n    const bm25Results = bm25Index.search(query, topK * 3);\n    const bm25Scores = new Map<string, number>();\n    \n    for (const result of bm25Results) {\n      bm25Scores.set(result.id, normalizeScore(result.score, 3));\n    }\n\n    // Calculate hybrid scores for all chunks\n    const results: SearchResult[] = [];\n\n    for (const { filepath, chunk, embedding } of allChunksData) {\n      const semanticScore = cosineSimilarity(queryEmbedding, embedding);\n      const bm25Score = bm25Scores.get(chunk.id) || 0;\n      \n      // Hybrid score: weighted combination of semantic and BM25\n      const hybridScore = (SEMANTIC_WEIGHT * semanticScore) + (BM25_WEIGHT * bm25Score);\n\n      if (hybridScore >= minScore || bm25Score > 0.3) {\n        results.push({\n          filepath,\n          chunk,\n          score: hybridScore,\n          moduleId: this.id,\n          context: {\n            semanticScore,\n            bm25Score,\n          },\n        });\n      }\n    }\n\n    // Sort by score descending and take top K\n    results.sort((a, b) => b.score - a.score);\n    return results.slice(0, topK);\n  }\n\n  private extractReferences(content: string, filepath: string): string[] {\n    const references: string[] = [];\n\n    // Extract import statements\n    const importRegex = /import\\s+.*?\\s+from\\s+['\"]([^'\"]+)['\"]/g;\n    const requireRegex = /require\\s*\\(\\s*['\"]([^'\"]+)['\"]\\s*\\)/g;\n\n    let match;\n    while ((match = importRegex.exec(content)) !== null) {\n      const importPath = match[1];\n      if (importPath.startsWith('.')) {\n        const dir = path.dirname(filepath);\n        const resolved = path.normalize(path.join(dir, importPath));\n        references.push(resolved);\n      }\n    }\n\n    while ((match = requireRegex.exec(content)) !== null) {\n      const importPath = match[1];\n      if (importPath.startsWith('.')) {\n        const dir = path.dirname(filepath);\n        const resolved = path.normalize(path.join(dir, importPath));\n        references.push(resolved);\n      }\n    }\n\n    return references;\n  }\n}\n",
+    "// Module registry - manages available index modules\nimport { IndexModule, ModuleRegistry, Config } from '../types';\n\nclass ModuleRegistryImpl implements ModuleRegistry {\n  private modules = new Map<string, IndexModule>();\n\n  register(module: IndexModule): void {\n    if (this.modules.has(module.id)) {\n      console.warn(`Module '${module.id}' is already registered, overwriting...`);\n    }\n    this.modules.set(module.id, module);\n  }\n\n  get(id: string): IndexModule | undefined {\n    return this.modules.get(id);\n  }\n\n  list(): IndexModule[] {\n    return Array.from(this.modules.values());\n  }\n\n  getEnabled(config: Config): IndexModule[] {\n    const enabledIds = new Set(\n      config.modules\n        .filter(m => m.enabled)\n        .map(m => m.id)\n    );\n    \n    return this.list().filter(m => enabledIds.has(m.id));\n  }\n}\n\n// Global singleton registry\nexport const registry: ModuleRegistry = new ModuleRegistryImpl();\n\n// Auto-register built-in modules\nexport async function registerBuiltInModules(): Promise<void> {\n  // Dynamic import to avoid circular dependencies\n  const { SemanticModule } = await import('./semantic');\n  registry.register(new SemanticModule());\n}\n",
+    "// Main indexer - coordinates modules for indexing files\nimport { glob } from 'glob';\nimport * as fs from 'fs/promises';\nimport * as path from 'path';\nimport {\n  Config,\n  IndexContext,\n  IndexModule,\n  ModuleManifest,\n  GlobalManifest,\n  FileIndex,\n} from '../types';\nimport {\n  DEFAULT_CONFIG,\n  loadConfig,\n  getModuleIndexPath,\n  getModuleManifestPath,\n  getGlobalManifestPath,\n  getModuleConfig,\n} from '../utils/config';\nimport { registry, registerBuiltInModules } from '../modules/registry';\nimport { EmbeddingModelName } from '../utils/embeddings';\n\nexport interface IndexResult {\n  moduleId: string;\n  indexed: number;\n  skipped: number;\n  errors: number;\n}\n\nexport interface IndexOptions {\n  /** Override the embedding model (semantic module) */\n  model?: EmbeddingModelName;\n  /** Show detailed progress */\n  verbose?: boolean;\n}\n\nexport interface CleanupResult {\n  moduleId: string;\n  /** Number of stale entries removed */\n  removed: number;\n  /** Number of valid entries kept */\n  kept: number;\n}\n\n/**\n * Index a directory using all enabled modules\n */\nexport async function indexDirectory(rootDir: string, options: IndexOptions = {}): Promise<IndexResult[]> {\n  const verbose = options.verbose ?? false;\n  \n  // Ensure absolute path\n  rootDir = path.resolve(rootDir);\n  \n  console.log(`Indexing directory: ${rootDir}`);\n\n  // Load config\n  const config = await loadConfig(rootDir);\n\n  // Register built-in modules\n  await registerBuiltInModules();\n\n  // Get enabled modules\n  const enabledModules = registry.getEnabled(config);\n\n  if (enabledModules.length === 0) {\n    console.log('No modules enabled. Check your configuration.');\n    return [];\n  }\n\n  console.log(`Enabled modules: ${enabledModules.map((m) => m.id).join(', ')}`);\n\n  // Get all files matching extensions\n  const files = await findFiles(rootDir, config);\n  console.log(`Found ${files.length} files to index`);\n\n  // Index with each module\n  const results: IndexResult[] = [];\n\n  for (const module of enabledModules) {\n    console.log(`\\n[${module.name}] Starting indexing...`);\n\n    // Initialize module if needed\n    const moduleConfig = getModuleConfig(config, module.id);\n    if (module.initialize && moduleConfig) {\n      // Apply CLI overrides to module config\n      const configWithOverrides = { ...moduleConfig };\n      if (options.model && module.id === 'semantic') {\n        configWithOverrides.options = {\n          ...configWithOverrides.options,\n          embeddingModel: options.model,\n        };\n      }\n      await module.initialize(configWithOverrides);\n    }\n\n    const result = await indexWithModule(rootDir, files, module, config, verbose);\n    results.push(result);\n\n    // Call finalize to build secondary indexes (Tier 1, BM25, etc.)\n    if (module.finalize) {\n      console.log(`[${module.name}] Building secondary indexes...`);\n      const ctx: IndexContext = {\n        rootDir,\n        config,\n        readFile: async (filepath: string) => {\n          const fullPath = path.isAbsolute(filepath) ? filepath : path.join(rootDir, filepath);\n          return fs.readFile(fullPath, 'utf-8');\n        },\n        getFileStats: async (filepath: string) => {\n          const fullPath = path.isAbsolute(filepath) ? filepath : path.join(rootDir, filepath);\n          const stats = await fs.stat(fullPath);\n          return { lastModified: stats.mtime.toISOString() };\n        },\n      };\n      await module.finalize(ctx);\n    }\n\n    console.log(`[${module.name}] Complete: ${result.indexed} indexed, ${result.skipped} skipped, ${result.errors} errors`);\n  }\n\n  // Update global manifest\n  await updateGlobalManifest(rootDir, enabledModules, config);\n\n  return results;\n}\n\n/**\n * Index files with a specific module\n */\nasync function indexWithModule(\n  rootDir: string,\n  files: string[],\n  module: IndexModule,\n  config: Config,\n  verbose: boolean\n): Promise<IndexResult> {\n  const result: IndexResult = {\n    moduleId: module.id,\n    indexed: 0,\n    skipped: 0,\n    errors: 0,\n  };\n\n  // Load existing manifest for this module\n  const manifest = await loadModuleManifest(rootDir, module.id, config);\n\n  // Create index context\n  const ctx: IndexContext = {\n    rootDir,\n    config,\n    readFile: async (filepath: string) => {\n      const fullPath = path.isAbsolute(filepath) ? filepath : path.join(rootDir, filepath);\n      return fs.readFile(fullPath, 'utf-8');\n    },\n    getFileStats: async (filepath: string) => {\n      const fullPath = path.isAbsolute(filepath) ? filepath : path.join(rootDir, filepath);\n      const stats = await fs.stat(fullPath);\n      return { lastModified: stats.mtime.toISOString() };\n    },\n  };\n\n  // Process each file\n  for (const filepath of files) {\n    const relativePath = path.relative(rootDir, filepath);\n    \n    try {\n      const stats = await fs.stat(filepath);\n      const lastModified = stats.mtime.toISOString();\n\n      // Check if file needs re-indexing\n      const existingEntry = manifest.files[relativePath];\n      if (existingEntry && existingEntry.lastModified === lastModified) {\n        if (verbose) {\n          console.log(`  Skipped ${relativePath} (unchanged)`);\n        }\n        result.skipped++;\n        continue;\n      }\n\n      // Read and index file\n      const content = await fs.readFile(filepath, 'utf-8');\n      \n      if (verbose) {\n        console.log(`  Processing ${relativePath}...`);\n      }\n      const fileIndex = await module.indexFile(relativePath, content, ctx);\n\n      if (!fileIndex) {\n        if (verbose) {\n          console.log(`  Skipped ${relativePath} (no chunks)`);\n        }\n        result.skipped++;\n        continue;\n      }\n\n      // Write index file\n      await writeFileIndex(rootDir, module.id, relativePath, fileIndex, config);\n\n      // Update manifest\n      manifest.files[relativePath] = {\n        lastModified,\n        chunkCount: fileIndex.chunks.length,\n      };\n\n      result.indexed++;\n    } catch (error) {\n      console.error(`  Error indexing ${relativePath}:`, error);\n      result.errors++;\n    }\n  }\n\n  // Update manifest\n  manifest.lastUpdated = new Date().toISOString();\n  await writeModuleManifest(rootDir, module.id, manifest, config);\n\n  return result;\n}\n\nasync function findFiles(rootDir: string, config: Config): Promise<string[]> {\n  const patterns = config.extensions.map((ext) => `**/*${ext}`);\n  const ignorePatterns = config.ignorePaths.map((p) => `**/${p}/**`);\n\n  const files: string[] = [];\n  for (const pattern of patterns) {\n    const matches = await glob(pattern, {\n      cwd: rootDir,\n      absolute: true,\n      ignore: ignorePatterns,\n    });\n    files.push(...matches);\n  }\n\n  return [...new Set(files)]; // Remove duplicates\n}\n\nasync function loadModuleManifest(\n  rootDir: string,\n  moduleId: string,\n  config: Config\n): Promise<ModuleManifest> {\n  const manifestPath = getModuleManifestPath(rootDir, moduleId, config);\n\n  try {\n    const content = await fs.readFile(manifestPath, 'utf-8');\n    return JSON.parse(content);\n  } catch {\n    return {\n      moduleId,\n      version: '1.0.0',\n      lastUpdated: new Date().toISOString(),\n      files: {},\n    };\n  }\n}\n\nasync function writeModuleManifest(\n  rootDir: string,\n  moduleId: string,\n  manifest: ModuleManifest,\n  config: Config\n): Promise<void> {\n  const manifestPath = getModuleManifestPath(rootDir, moduleId, config);\n  await fs.mkdir(path.dirname(manifestPath), { recursive: true });\n  await fs.writeFile(manifestPath, JSON.stringify(manifest, null, 2));\n}\n\nasync function writeFileIndex(\n  rootDir: string,\n  moduleId: string,\n  filepath: string,\n  fileIndex: FileIndex,\n  config: Config\n): Promise<void> {\n  const indexPath = getModuleIndexPath(rootDir, moduleId, config);\n  const indexFilePath = path.join(indexPath, filepath.replace(/\\.[^.]+$/, '.json'));\n\n  await fs.mkdir(path.dirname(indexFilePath), { recursive: true });\n  await fs.writeFile(indexFilePath, JSON.stringify(fileIndex, null, 2));\n}\n\nasync function updateGlobalManifest(\n  rootDir: string,\n  modules: IndexModule[],\n  config: Config\n): Promise<void> {\n  const manifestPath = getGlobalManifestPath(rootDir, config);\n\n  const manifest: GlobalManifest = {\n    version: config.version,\n    lastUpdated: new Date().toISOString(),\n    modules: modules.map((m) => m.id),\n  };\n\n  await fs.mkdir(path.dirname(manifestPath), { recursive: true });\n  await fs.writeFile(manifestPath, JSON.stringify(manifest, null, 2));\n}\n\n/**\n * Clean up stale index entries for files that no longer exist\n * @param rootDir - Root directory of the project\n * @param options - Cleanup options\n * @returns Array of cleanup results per module\n */\nexport async function cleanupIndex(\n  rootDir: string, \n  options: { verbose?: boolean } = {}\n): Promise<CleanupResult[]> {\n  const verbose = options.verbose ?? false;\n  \n  // Ensure absolute path\n  rootDir = path.resolve(rootDir);\n  \n  console.log(`Cleaning up index in: ${rootDir}`);\n\n  // Load config\n  const config = await loadConfig(rootDir);\n\n  // Register built-in modules\n  await registerBuiltInModules();\n\n  // Get enabled modules\n  const enabledModules = registry.getEnabled(config);\n\n  if (enabledModules.length === 0) {\n    console.log('No modules enabled.');\n    return [];\n  }\n\n  const results: CleanupResult[] = [];\n\n  for (const module of enabledModules) {\n    console.log(`\\n[${module.name}] Checking for stale entries...`);\n    \n    const result = await cleanupModuleIndex(rootDir, module.id, config, verbose);\n    results.push(result);\n    \n    console.log(`[${module.name}] Removed ${result.removed} stale entries, kept ${result.kept} valid entries`);\n  }\n\n  return results;\n}\n\n/**\n * Clean up stale index entries for a specific module\n */\nasync function cleanupModuleIndex(\n  rootDir: string,\n  moduleId: string,\n  config: Config,\n  verbose: boolean\n): Promise<CleanupResult> {\n  const result: CleanupResult = {\n    moduleId,\n    removed: 0,\n    kept: 0,\n  };\n\n  // Load manifest\n  const manifest = await loadModuleManifest(rootDir, moduleId, config);\n  const indexPath = getModuleIndexPath(rootDir, moduleId, config);\n  \n  const filesToRemove: string[] = [];\n  const updatedFiles: ModuleManifest['files'] = {};\n\n  // Check each indexed file\n  for (const [filepath, entry] of Object.entries(manifest.files)) {\n    const fullPath = path.join(rootDir, filepath);\n    \n    try {\n      await fs.access(fullPath);\n      // File exists, keep it\n      updatedFiles[filepath] = entry;\n      result.kept++;\n    } catch {\n      // File doesn't exist, mark for removal\n      filesToRemove.push(filepath);\n      result.removed++;\n      \n      if (verbose) {\n        console.log(`  Removing stale entry: ${filepath}`);\n      }\n    }\n  }\n\n  // Remove stale index files\n  for (const filepath of filesToRemove) {\n    const indexFilePath = path.join(indexPath, filepath.replace(/\\.[^.]+$/, '.json'));\n    try {\n      await fs.unlink(indexFilePath);\n    } catch {\n      // Index file may not exist, that's okay\n    }\n  }\n\n  // Update manifest with only valid files\n  manifest.files = updatedFiles;\n  manifest.lastUpdated = new Date().toISOString();\n  await writeModuleManifest(rootDir, moduleId, manifest, config);\n\n  // Clean up empty directories in the index\n  await cleanupEmptyDirectories(indexPath);\n\n  return result;\n}\n\n/**\n * Recursively remove empty directories\n */\nasync function cleanupEmptyDirectories(dir: string): Promise<boolean> {\n  try {\n    const entries = await fs.readdir(dir, { withFileTypes: true });\n    \n    // Process subdirectories first\n    for (const entry of entries) {\n      if (entry.isDirectory()) {\n        const subDir = path.join(dir, entry.name);\n        await cleanupEmptyDirectories(subDir);\n      }\n    }\n    \n    // Check if directory is now empty (re-read after potential subdirectory removal)\n    const remainingEntries = await fs.readdir(dir);\n    \n    // Don't remove the root index directory or manifest files\n    if (remainingEntries.length === 0) {\n      await fs.rmdir(dir);\n      return true;\n    }\n    \n    return false;\n  } catch {\n    return false;\n  }\n}\n",
+    "// Search module - queries across all enabled modules\nimport * as fs from 'fs/promises';\nimport * as path from 'path';\nimport {\n  Config,\n  SearchContext,\n  SearchOptions,\n  SearchResult,\n  FileIndex,\n  IndexModule,\n  GlobalManifest,\n} from '../types';\nimport {\n  loadConfig,\n  getModuleIndexPath,\n  getGlobalManifestPath,\n  getModuleConfig,\n} from '../utils/config';\nimport { registry, registerBuiltInModules } from '../modules/registry';\n\n/**\n * Search across all enabled modules\n */\nexport async function search(\n  rootDir: string,\n  query: string,\n  options: SearchOptions = {}\n): Promise<SearchResult[]> {\n  // Ensure absolute path\n  rootDir = path.resolve(rootDir);\n\n  console.log(`Searching for: \"${query}\"`);\n\n  // Load config\n  const config = await loadConfig(rootDir);\n\n  // Register built-in modules\n  await registerBuiltInModules();\n\n  // Check which modules have indexes\n  const globalManifest = await loadGlobalManifest(rootDir, config);\n  \n  if (!globalManifest || globalManifest.modules.length === 0) {\n    console.log('No index found. Run \"bun run index\" first.');\n    return [];\n  }\n\n  // Get modules that are both enabled and have indexes\n  const modulesToSearch: IndexModule[] = [];\n  \n  for (const moduleId of globalManifest.modules) {\n    const module = registry.get(moduleId);\n    const moduleConfig = getModuleConfig(config, moduleId);\n    \n    if (module && moduleConfig?.enabled) {\n      // Initialize module if needed\n      if (module.initialize) {\n        await module.initialize(moduleConfig);\n      }\n      modulesToSearch.push(module);\n    }\n  }\n\n  if (modulesToSearch.length === 0) {\n    console.log('No enabled modules with indexes found.');\n    return [];\n  }\n\n  // Search with each module and aggregate results\n  const allResults: SearchResult[] = [];\n\n  for (const module of modulesToSearch) {\n    const ctx = createSearchContext(rootDir, module.id, config);\n    const moduleResults = await module.search(query, ctx, options);\n    allResults.push(...moduleResults);\n  }\n\n  // Sort all results by score\n  allResults.sort((a, b) => b.score - a.score);\n\n  // Return top K\n  const topK = options.topK ?? 10;\n  return allResults.slice(0, topK);\n}\n\n/**\n * Create a search context for a specific module\n */\nfunction createSearchContext(\n  rootDir: string,\n  moduleId: string,\n  config: Config\n): SearchContext {\n  const indexPath = getModuleIndexPath(rootDir, moduleId, config);\n\n  return {\n    rootDir,\n    config,\n    \n    loadFileIndex: async (filepath: string): Promise<FileIndex | null> => {\n      // filepath may or may not have an extension\n      // If it has an extension, replace it with .json; otherwise append .json\n      const hasExtension = /\\.[^./]+$/.test(filepath);\n      const indexFilePath = hasExtension\n        ? path.join(indexPath, filepath.replace(/\\.[^.]+$/, '.json'))\n        : path.join(indexPath, filepath + '.json');\n      \n      try {\n        const content = await fs.readFile(indexFilePath, 'utf-8');\n        return JSON.parse(content);\n      } catch {\n        return null;\n      }\n    },\n    \n    listIndexedFiles: async (): Promise<string[]> => {\n      const files: string[] = [];\n      await traverseDirectory(indexPath, files, indexPath);\n      \n      // Convert index file paths back to source file paths\n      return files\n        .filter(f => f.endsWith('.json') && !f.endsWith('manifest.json'))\n        .map(f => {\n          const relative = path.relative(indexPath, f);\n          // Convert .json back to original extension (we'll handle this generically)\n          return relative.replace(/\\.json$/, '');\n        });\n    },\n  };\n}\n\nasync function traverseDirectory(dir: string, files: string[], basePath: string): Promise<void> {\n  try {\n    const entries = await fs.readdir(dir, { withFileTypes: true });\n\n    for (const entry of entries) {\n      const fullPath = path.join(dir, entry.name);\n\n      if (entry.isDirectory()) {\n        await traverseDirectory(fullPath, files, basePath);\n      } else if (entry.isFile()) {\n        files.push(fullPath);\n      }\n    }\n  } catch {\n    // Directory doesn't exist\n  }\n}\n\nasync function loadGlobalManifest(rootDir: string, config: Config): Promise<GlobalManifest | null> {\n  const manifestPath = getGlobalManifestPath(rootDir, config);\n\n  try {\n    const content = await fs.readFile(manifestPath, 'utf-8');\n    return JSON.parse(content);\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Format search results for display\n * @param results - Array of search results to format\n * @returns Formatted string for console output\n */\nexport function formatSearchResults(results: SearchResult[]): string {\n  if (results.length === 0) {\n    return 'No results found.';\n  }\n\n  let output = `Found ${results.length} results:\\n\\n`;\n\n  for (let i = 0; i < results.length; i++) {\n    const result = results[i];\n    const { chunk } = result;\n    \n    // Format location with optional name\n    const location = `${result.filepath}:${chunk.startLine}-${chunk.endLine}`;\n    const nameInfo = chunk.name ? ` (${chunk.name})` : '';\n    \n    output += `${i + 1}. ${location}${nameInfo}\\n`;\n    output += `   Score: ${(result.score * 100).toFixed(1)}% | Type: ${chunk.type}`;\n    \n    // Add export indicator\n    if (chunk.isExported) {\n      output += ' | exported';\n    }\n    output += '\\n';\n\n    // Show preview (first 3 lines)\n    const lines = chunk.content.split('\\n').slice(0, 3);\n    for (const line of lines) {\n      const trimmedLine = line.substring(0, 80);\n      output += `      ${trimmedLine}${line.length > 80 ? '...' : ''}\\n`;\n    }\n\n    output += '\\n';\n  }\n\n  return output;\n}\n",
+    "// Main CLI entry point for raggrep\n\nimport { EMBEDDING_MODELS, getCacheDir, type EmbeddingModelName } from '../utils/embeddings';\n\nconst args = process.argv.slice(2);\nconst command = args[0];\n\n/**\n * Parsed CLI flags from command line arguments\n */\ninterface ParsedFlags {\n  /** Embedding model to use */\n  model?: EmbeddingModelName;\n  /** Number of results to return */\n  topK?: number;\n  /** Minimum similarity score threshold (0-1) */\n  minScore?: number;\n  /** File extension filter (e.g., 'ts', 'tsx') */\n  fileType?: string;\n  /** Show help message */\n  help: boolean;\n  /** Show detailed progress */\n  verbose: boolean;\n  /** Remaining positional arguments */\n  remaining: string[];\n}\n\n/**\n * Parse CLI flags from command line arguments\n * @param args - Array of command line arguments (excluding command name)\n * @returns Parsed flags object\n */\nfunction parseFlags(args: string[]): ParsedFlags {\n  const flags: ParsedFlags = {\n    help: false,\n    verbose: false,\n    remaining: [],\n  };\n  \n  for (let i = 0; i < args.length; i++) {\n    const arg = args[i];\n    \n    if (arg === '--help' || arg === '-h') {\n      flags.help = true;\n    } else if (arg === '--verbose' || arg === '-v') {\n      flags.verbose = true;\n    } else if (arg === '--model' || arg === '-m') {\n      const modelName = args[++i];\n      if (modelName && modelName in EMBEDDING_MODELS) {\n        flags.model = modelName as EmbeddingModelName;\n      } else {\n        console.error(`Invalid model: ${modelName}`);\n        console.error(`Available models: ${Object.keys(EMBEDDING_MODELS).join(', ')}`);\n        process.exit(1);\n      }\n    } else if (arg === '--top' || arg === '-k') {\n      const k = parseInt(args[++i], 10);\n      if (!isNaN(k) && k > 0) {\n        flags.topK = k;\n      }\n    } else if (arg === '--min-score' || arg === '-s') {\n      const score = parseFloat(args[++i]);\n      if (!isNaN(score) && score >= 0 && score <= 1) {\n        flags.minScore = score;\n      } else {\n        console.error(`Invalid min-score: ${args[i]}. Must be a number between 0 and 1.`);\n        process.exit(1);\n      }\n    } else if (arg === '--type' || arg === '-t') {\n      const type = args[++i];\n      if (type) {\n        // Normalize: remove leading dot if present\n        flags.fileType = type.startsWith('.') ? type.slice(1) : type;\n      } else {\n        console.error('--type requires a file extension (e.g., ts, tsx, js)');\n        process.exit(1);\n      }\n    } else if (!arg.startsWith('-')) {\n      flags.remaining.push(arg);\n    }\n  }\n  \n  return flags;\n}\n\nasync function main() {\n  const flags = parseFlags(args.slice(1)); // Skip the command itself\n  \n  switch (command) {\n    case 'index': {\n      if (flags.help) {\n        const models = Object.keys(EMBEDDING_MODELS).join(', ');\n        console.log(`\nraggrep index - Index the current directory for semantic search\n\nUsage:\n  raggrep index [options]\n\nOptions:\n  -m, --model <name>   Embedding model to use (default: all-MiniLM-L6-v2)\n  -v, --verbose        Show detailed progress\n  -h, --help           Show this help message\n\nAvailable Models:\n  ${models}\n\nModel Cache: ${getCacheDir()}\n\nExamples:\n  raggrep index\n  raggrep index --model bge-small-en-v1.5\n  raggrep index --verbose\n`);\n        process.exit(0);\n      }\n\n      const { indexDirectory } = await import('../indexer');\n      console.log('RAGgrep Indexer');\n      console.log('================\\n');\n      try {\n        const results = await indexDirectory(process.cwd(), { \n          model: flags.model,\n          verbose: flags.verbose,\n        });\n        console.log('\\n================');\n        console.log('Summary:');\n        for (const result of results) {\n          console.log(`  ${result.moduleId}: ${result.indexed} indexed, ${result.skipped} skipped, ${result.errors} errors`);\n        }\n      } catch (error) {\n        console.error('Error during indexing:', error);\n        process.exit(1);\n      }\n      break;\n    }\n\n    case 'query': {\n      if (flags.help) {\n        console.log(`\nraggrep query - Search the indexed codebase\n\nUsage:\n  raggrep query <search query> [options]\n\nOptions:\n  -k, --top <n>        Number of results to return (default: 10)\n  -s, --min-score <n>  Minimum similarity score 0-1 (default: 0.15)\n  -t, --type <ext>     Filter by file extension (e.g., ts, tsx, js)\n  -h, --help           Show this help message\n\nExamples:\n  raggrep query \"user authentication\"\n  raggrep query \"handle errors\" --top 5\n  raggrep query \"database\" --min-score 0.1\n  raggrep query \"interface\" --type ts\n`);\n        process.exit(0);\n      }\n\n      const { search, formatSearchResults } = await import('../search');\n      const query = flags.remaining[0];\n      \n      if (!query) {\n        console.error('Usage: raggrep query <search query>');\n        console.error('Run \"raggrep query --help\" for more information.');\n        process.exit(1);\n      }\n      \n      console.log('RAGgrep Search');\n      console.log('==============\\n');\n      try {\n        // Build file patterns if type filter specified\n        const filePatterns = flags.fileType ? [`*.${flags.fileType}`] : undefined;\n        \n        const results = await search(process.cwd(), query, { \n          topK: flags.topK ?? 10,\n          minScore: flags.minScore,\n          filePatterns,\n        });\n        console.log(formatSearchResults(results));\n      } catch (error) {\n        console.error('Error during search:', error);\n        process.exit(1);\n      }\n      break;\n    }\n\n    case 'cleanup': {\n      if (flags.help) {\n        console.log(`\nraggrep cleanup - Remove stale index entries for deleted files\n\nUsage:\n  raggrep cleanup [options]\n\nOptions:\n  -v, --verbose        Show detailed progress\n  -h, --help           Show this help message\n\nDescription:\n  Scans the index and removes entries for files that no longer exist.\n  Run this command after deleting files to clean up the index.\n\nExamples:\n  raggrep cleanup\n  raggrep cleanup --verbose\n`);\n        process.exit(0);\n      }\n\n      const { cleanupIndex } = await import('../indexer');\n      console.log('RAGgrep Cleanup');\n      console.log('===============\\n');\n      try {\n        const results = await cleanupIndex(process.cwd(), { \n          verbose: flags.verbose,\n        });\n        console.log('\\n===============');\n        console.log('Summary:');\n        for (const result of results) {\n          console.log(`  ${result.moduleId}: ${result.removed} removed, ${result.kept} kept`);\n        }\n      } catch (error) {\n        console.error('Error during cleanup:', error);\n        process.exit(1);\n      }\n      break;\n    }\n\n    default:\n      console.log(`\nraggrep - Local filesystem-based RAG system for codebases\n\nUsage:\n  raggrep <command> [options]\n\nCommands:\n  index    Index the current directory\n  query    Search the indexed codebase\n  cleanup  Remove stale index entries for deleted files\n\nOptions:\n  -h, --help   Show help for a command\n\nExamples:\n  raggrep index\n  raggrep index --model bge-small-en-v1.5\n  raggrep query \"user login\"\n  raggrep query \"handle errors\" --top 5\n  raggrep cleanup\n\nRun 'raggrep <command> --help' for more information.\n`);\n      if (command && command !== '--help' && command !== '-h') {\n        console.error(`Unknown command: ${command}`);\n        process.exit(1);\n      }\n  }\n}\n\nmain();\n"
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+  "debugId": "8E6C629D8A1BA14F64756E2164756E21",
+  "names": []
+}

package/dist/composition.d.ts

@@ -0,0 +1,52 @@
+/**
+ * Composition Root
+ *
+ * This is the single place where all dependencies are wired together.
+ * The composition root creates concrete implementations and injects them
+ * into use cases and services.
+ *
+ * This is the only file that knows about concrete implementations.
+ * Everything else depends only on interfaces (ports).
+ */
+import type { Config } from './domain/entities';
+import type { FileSystem } from './domain/ports';
+import type { IndexModule, IndexContext, SearchContext } from './types';
+import { FileIndexStorage } from './infrastructure/storage';
+/**
+ * Container for all application services.
+ * Created once and passed to use cases.
+ */
+export interface ServiceContainer {
+    fileSystem: FileSystem;
+    storage: FileIndexStorage;
+    getEnabledModules: (config: Config) => IndexModule[];
+    getModule: (moduleId: string) => IndexModule | undefined;
+    initializeModule: (module: IndexModule, config: Config) => Promise<void>;
+}
+/**
+ * Create a service container for a specific project directory.
+ */
+export declare function createServiceContainer(rootDir: string): Promise<ServiceContainer>;
+import type { IndexDirectoryDependencies } from './application/usecases/indexDirectory';
+import type { SearchIndexDependencies } from './application/usecases/searchIndex';
+import type { CleanupIndexDependencies } from './application/usecases/cleanupIndex';
+/**
+ * Create dependencies for the indexDirectory use case.
+ */
+export declare function createIndexDependencies(container: ServiceContainer): IndexDirectoryDependencies;
+/**
+ * Create dependencies for the searchIndex use case.
+ */
+export declare function createSearchDependencies(container: ServiceContainer): SearchIndexDependencies;
+/**
+ * Create dependencies for the cleanupIndex use case.
+ */
+export declare function createCleanupDependencies(container: ServiceContainer): CleanupIndexDependencies;
+/**
+ * Create an IndexContext for a module.
+ */
+export declare function createIndexContext(rootDir: string, config: Config, fileSystem: FileSystem): IndexContext;
+/**
+ * Create a SearchContext for a module.
+ */
+export declare function createSearchContext(rootDir: string, moduleId: string, config: Config, storage: FileIndexStorage): SearchContext;

package/dist/domain/entities/chunk.d.ts

@@ -0,0 +1,41 @@
+/**
+ * Chunk Entity
+ *
+ * Represents a semantic unit of code that can be indexed and searched.
+ * This is a core domain entity with no external dependencies.
+ */
+/**
+ * Types of code chunks that can be extracted from source files.
+ */
+export type ChunkType = 'function' | 'class' | 'interface' | 'type' | 'enum' | 'variable' | 'block' | 'file';
+/**
+ * A chunk of code or text that has been parsed and can be indexed.
+ *
+ * Chunks are the fundamental unit of indexing in RAGgrep. Each chunk
+ * represents a meaningful code construct (function, class, etc.) that
+ * can be independently searched and retrieved.
+ */
+export interface Chunk {
+    /** Unique identifier for this chunk (typically filepath + line range) */
+    id: string;
+    /** The source code content */
+    content: string;
+    /** 1-based start line number in the source file */
+    startLine: number;
+    /** 1-based end line number in the source file */
+    endLine: number;
+    /** The type of code construct */
+    type: ChunkType;
+    /** Name of the construct (function name, class name, etc.) */
+    name?: string;
+    /** Whether this chunk is exported from its module */
+    isExported?: boolean;
+    /** JSDoc comment if present */
+    jsDoc?: string;
+    /** Additional metadata for extensibility */
+    metadata?: Record<string, unknown>;
+}
+/**
+ * Generate a unique chunk ID from filepath and line numbers.
+ */
+export declare function createChunkId(filepath: string, startLine: number, endLine: number): string;

package/dist/domain/entities/config.d.ts

@@ -0,0 +1,43 @@
+/**
+ * Config Entity
+ *
+ * Configuration for RAGgrep indexing and search operations.
+ */
+/**
+ * Configuration for a specific index module.
+ */
+export interface ModuleConfig {
+    /** Unique module identifier */
+    id: string;
+    /** Whether the module is enabled */
+    enabled: boolean;
+    /** Module-specific options */
+    options?: Record<string, unknown>;
+}
+/**
+ * Main RAGgrep configuration.
+ */
+export interface Config {
+    /** RAGgrep version */
+    version: string;
+    /** Directory name for index storage (default: '.raggrep') */
+    indexDir: string;
+    /** File extensions to index (e.g., ['.ts', '.tsx', '.js']) */
+    extensions: string[];
+    /** Paths to ignore during indexing */
+    ignorePaths: string[];
+    /** Enabled modules and their configurations */
+    modules: ModuleConfig[];
+}
+/**
+ * Default paths to ignore during indexing.
+ */
+export declare const DEFAULT_IGNORE_PATHS: string[];
+/**
+ * Default file extensions to index.
+ */
+export declare const DEFAULT_EXTENSIONS: string[];
+/**
+ * Create a default configuration.
+ */
+export declare function createDefaultConfig(): Config;

package/dist/domain/entities/fileIndex.d.ts

@@ -0,0 +1,58 @@
+/**
+ * FileIndex Entity
+ *
+ * Represents the indexed data for a single source file.
+ * This is a Tier 2 index structure containing full chunk data and embeddings.
+ */
+import type { Chunk } from './chunk';
+/**
+ * Indexed data for a single file (Tier 2 index).
+ *
+ * Contains all chunks extracted from the file along with
+ * module-specific data like embeddings.
+ */
+export interface FileIndex {
+    /** Relative path to the source file */
+    filepath: string;
+    /** ISO timestamp of when the file was last modified */
+    lastModified: string;
+    /** Chunks extracted from the file */
+    chunks: Chunk[];
+    /** Module-specific indexed data (e.g., embeddings, symbol tables) */
+    moduleData: Record<string, unknown>;
+    /** References to other files (imports, requires) */
+    references?: string[];
+}
+/**
+ * Manifest entry for a single indexed file.
+ */
+export interface FileManifestEntry {
+    /** ISO timestamp of when the file was last modified */
+    lastModified: string;
+    /** Number of chunks in the file */
+    chunkCount: number;
+}
+/**
+ * Manifest tracking all indexed files for a specific module.
+ */
+export interface ModuleManifest {
+    /** Module identifier */
+    moduleId: string;
+    /** Module version (for compatibility checking) */
+    version: string;
+    /** ISO timestamp of last update */
+    lastUpdated: string;
+    /** Map of filepath to manifest entry */
+    files: Record<string, FileManifestEntry>;
+}
+/**
+ * Global manifest tracking all active modules.
+ */
+export interface GlobalManifest {
+    /** RAGgrep version */
+    version: string;
+    /** ISO timestamp of last update */
+    lastUpdated: string;
+    /** List of active module IDs */
+    modules: string[];
+}

package/dist/domain/entities/fileSummary.d.ts

@@ -0,0 +1,61 @@
+/**
+ * FileSummary Entity
+ *
+ * Lightweight file summary for the symbolic index.
+ * Used for fast keyword-based filtering before loading full file indexes.
+ *
+ * Stored as individual files in: .raggrep/index/<module>/symbolic/<filepath>.json
+ */
+import type { ChunkType } from "./chunk";
+/**
+ * Lightweight file summary for fast filtering.
+ *
+ * Contains just enough information to decide if a file
+ * is a candidate for more detailed semantic search.
+ */
+export interface FileSummary {
+    /** Relative path to the source file */
+    filepath: string;
+    /** Number of chunks in this file */
+    chunkCount: number;
+    /** Types of chunks present (function, class, interface, etc.) */
+    chunkTypes: ChunkType[];
+    /** Extracted keywords from chunk names and content */
+    keywords: string[];
+    /** Names of exported symbols */
+    exports: string[];
+    /** ISO timestamp of when the file was last modified */
+    lastModified: string;
+}
+/**
+ * Metadata for the symbolic index.
+ * Stored in: .raggrep/index/<module>/symbolic/_meta.json
+ *
+ * Contains global BM25 statistics needed for keyword search.
+ * Individual FileSummary files are stored separately for scalability.
+ */
+export interface SymbolicIndexMeta {
+    /** Schema version */
+    version: string;
+    /** ISO timestamp of last update */
+    lastUpdated: string;
+    /** Module ID this index belongs to */
+    moduleId: string;
+    /** Number of indexed files */
+    fileCount: number;
+    /** Pre-computed BM25 data for keyword search */
+    bm25Data: {
+        /** Average document length */
+        avgDocLength: number;
+        /** Document frequencies for each term */
+        documentFrequencies: Record<string, number>;
+        /** Total number of documents */
+        totalDocs: number;
+    };
+}
+/**
+ * @deprecated Use SymbolicIndexMeta instead. Kept for backwards compatibility.
+ */
+export type Tier1Manifest = SymbolicIndexMeta & {
+    files: Record<string, FileSummary>;
+};

package/dist/domain/entities/index.d.ts

@@ -0,0 +1,14 @@
+/**
+ * Domain Entities
+ *
+ * Core business objects with no external dependencies.
+ * These represent the fundamental concepts in the RAGgrep domain.
+ */
+export type { Chunk, ChunkType } from "./chunk";
+export { createChunkId } from "./chunk";
+export type { FileIndex, FileManifestEntry, ModuleManifest, GlobalManifest, } from "./fileIndex";
+export type { FileSummary, SymbolicIndexMeta, Tier1Manifest, } from "./fileSummary";
+export type { SearchResult, SearchOptions } from "./searchResult";
+export { DEFAULT_SEARCH_OPTIONS } from "./searchResult";
+export type { Config, ModuleConfig } from "./config";
+export { DEFAULT_IGNORE_PATHS, DEFAULT_EXTENSIONS, createDefaultConfig, } from "./config";

package/dist/domain/entities/searchResult.d.ts

@@ -0,0 +1,36 @@
+/**
+ * SearchResult Entity
+ *
+ * Represents a single result from a search query.
+ */
+import type { Chunk } from './chunk';
+/**
+ * A search result with relevance score and source information.
+ */
+export interface SearchResult {
+    /** Path to the file containing the result */
+    filepath: string;
+    /** The matching chunk */
+    chunk: Chunk;
+    /** Relevance score (0-1, higher is better) */
+    score: number;
+    /** ID of the module that produced this result */
+    moduleId: string;
+    /** Additional context from the search (e.g., semantic vs keyword scores) */
+    context?: Record<string, unknown>;
+}
+/**
+ * Options for search operations.
+ */
+export interface SearchOptions {
+    /** Maximum number of results to return (default: 10) */
+    topK?: number;
+    /** Minimum similarity score threshold 0-1 (default: 0.15) */
+    minScore?: number;
+    /** Filter to specific file patterns (e.g., ['*.ts', '*.tsx']) */
+    filePatterns?: string[];
+}
+/**
+ * Default search options.
+ */
+export declare const DEFAULT_SEARCH_OPTIONS: Required<SearchOptions>;

package/dist/domain/index.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Domain Layer
+ *
+ * Contains the core business logic of RAGgrep:
+ * - Entities: Core data structures
+ * - Ports: Interfaces for external dependencies
+ * - Services: Pure business logic and algorithms
+ */
+export * from './entities';
+export * from './ports';
+export * from './services';