raggrep 0.1.0 → 0.1.3

package/dist/index.js.map

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../src/domain/entities/config.ts", "../src/domain/entities/index.ts", "../src/utils/embeddings.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/indexer/index.ts", "../src/modules/registry.ts", "../src/search/index.ts", "../src/index.ts"],
+  "sources": ["../src/domain/entities/config.ts", "../src/domain/entities/index.ts", "../src/utils/embeddings.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/indexer/index.ts", "../src/modules/registry.ts", "../src/indexer/watcher.ts", "../src/search/index.ts", "../src/index.ts"],
   "sourcesContent": [
     "/**\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",
@@ -8,15 +8,16 @@
     "/**\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 * 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 * Common architectural layer patterns in file names/paths.\n * Used to detect the layer a file belongs to.\n */\nexport const LAYER_PATTERNS: Record<string, string[]> = {\n  'controller': ['controller', 'controllers', 'handler', 'handlers', 'route', 'routes', 'api'],\n  'service': ['service', 'services', 'usecase', 'usecases', 'application'],\n  'repository': ['repository', 'repositories', 'repo', 'repos', 'dao', 'store', 'storage'],\n  'model': ['model', 'models', 'entity', 'entities', 'schema', 'schemas'],\n  'util': ['util', 'utils', 'utility', 'utilities', 'helper', 'helpers', 'common', 'shared'],\n  'config': ['config', 'configs', 'configuration', 'settings'],\n  'middleware': ['middleware', 'middlewares', 'interceptor', 'interceptors'],\n  'domain': ['domain', 'core', 'business'],\n  'infrastructure': ['infrastructure', 'infra', 'external', 'adapters'],\n  'presentation': ['presentation', 'view', 'views', 'component', 'components', 'ui'],\n  'test': ['test', 'tests', 'spec', 'specs', '__tests__', '__test__'],\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 * Split a string by camelCase, PascalCase, snake_case, and kebab-case.\n */\nfunction splitIdentifier(str: string): string[] {\n  return str\n    // Split camelCase and PascalCase\n    .replace(/([a-z])([A-Z])/g, '$1 $2')\n    // Split snake_case and kebab-case\n    .replace(/[_-]/g, ' ')\n    .split(/\\s+/)\n    .map(s => s.toLowerCase())\n    .filter(s => s.length > 1);\n}\n\n/**\n * Extract keywords from a file path.\n * \n * Enhanced extraction that:\n * - Splits camelCase/PascalCase filenames\n * - Extracts directory segments\n * - Recognizes common patterns (Service, Controller, etc.)\n * \n * @param filepath - File path to extract keywords from\n * @returns Array of keywords from path segments\n */\nexport function extractPathKeywords(filepath: string): string[] {\n  const keywords = new Set<string>();\n  \n  // Split path into segments (excluding extension)\n  const pathWithoutExt = filepath.replace(/\\.[^.]+$/, '');\n  const segments = pathWithoutExt.split(/[/\\\\]/);\n  \n  for (const segment of segments) {\n    if (segment.length < 2) continue;\n    \n    // Add the full segment\n    const lower = segment.toLowerCase();\n    if (!COMMON_KEYWORDS.has(lower) && lower.length > 2) {\n      keywords.add(lower);\n    }\n    \n    // Split camelCase/PascalCase/snake_case and add parts\n    const parts = splitIdentifier(segment);\n    for (const part of parts) {\n      if (!COMMON_KEYWORDS.has(part) && part.length > 2) {\n        keywords.add(part);\n      }\n    }\n  }\n  \n  return Array.from(keywords);\n}\n\n/**\n * Path context information extracted from a file path.\n */\nexport interface PathContext {\n  /** Directory segments (excluding filename) */\n  segments: string[];\n  /** Detected architectural layer (service, controller, repository, etc.) */\n  layer?: string;\n  /** Detected feature domain (auth, users, payments, etc.) */\n  domain?: string;\n  /** Path depth (number of directory levels) */\n  depth: number;\n  /** Keywords extracted from the path */\n  keywords: string[];\n}\n\n/**\n * Parse a file path and extract structural context.\n * \n * This helps with:\n * - Boosting files in related directories\n * - Understanding architectural layer\n * - Grouping by feature domain\n * \n * @param filepath - File path to parse\n * @returns Parsed path context\n */\nexport function parsePathContext(filepath: string): PathContext {\n  const pathWithoutExt = filepath.replace(/\\.[^.]+$/, '');\n  const allSegments = pathWithoutExt.split(/[/\\\\]/);\n  const filename = allSegments[allSegments.length - 1];\n  const dirSegments = allSegments.slice(0, -1);\n  \n  // Extract keywords from all segments\n  const keywords = extractPathKeywords(filepath);\n  \n  // Detect layer from filename and path\n  let layer: string | undefined;\n  const allLower = [...dirSegments, filename].map(s => s.toLowerCase()).join(' ');\n  const filenameLower = filename.toLowerCase();\n  \n  for (const [layerName, patterns] of Object.entries(LAYER_PATTERNS)) {\n    for (const pattern of patterns) {\n      // Check filename first (higher priority)\n      if (filenameLower.includes(pattern)) {\n        layer = layerName;\n        break;\n      }\n      // Check path segments\n      if (dirSegments.some(s => s.toLowerCase() === pattern)) {\n        layer = layerName;\n        break;\n      }\n    }\n    if (layer) break;\n  }\n  \n  // Detect domain from non-layer directory names\n  // e.g., src/services/auth/authService.ts → domain = \"auth\"\n  // Traverse from innermost to outermost to find the most specific domain\n  let domain: string | undefined;\n  const layerPatternSet = new Set(Object.values(LAYER_PATTERNS).flat());\n  \n  // Create a reversed copy to traverse from innermost to outermost\n  const reversedSegments = [...dirSegments].reverse();\n  for (const segment of reversedSegments) {\n    const lower = segment.toLowerCase();\n    // Skip common non-domain directories\n    if (['src', 'lib', 'app', 'packages', 'modules'].includes(lower)) continue;\n    // Skip layer directories\n    if (layerPatternSet.has(lower)) continue;\n    // This is likely the domain\n    if (lower.length > 2) {\n      domain = lower;\n      break;\n    }\n  }\n  \n  return {\n    segments: dirSegments,\n    layer,\n    domain,\n    depth: dirSegments.length,\n    keywords,\n  };\n}\n\n/**\n * Generate a path context string for embedding.\n * This is prepended to content to give the embedding model path awareness.\n * \n * @param pathContext - Parsed path context\n * @returns A string representation of the path context\n */\nexport function formatPathContextForEmbedding(pathContext: PathContext): string {\n  const parts: string[] = [];\n  \n  if (pathContext.domain) {\n    parts.push(pathContext.domain);\n  }\n  \n  if (pathContext.layer) {\n    parts.push(pathContext.layer);\n  }\n  \n  // Add significant path segments (limit to avoid noise)\n  const significantSegments = pathContext.segments\n    .slice(-3) // Last 3 directories\n    .filter(s => s.length > 2 && !['src', 'lib', 'app'].includes(s.toLowerCase()));\n  \n  if (significantSegments.length > 0) {\n    parts.push(...significantSegments.map(s => s.toLowerCase()));\n  }\n  \n  if (parts.length === 0) return '';\n  \n  // Deduplicate\n  const unique = [...new Set(parts)];\n  return `[${unique.join(' ')}]`;\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",
-    "// 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",
+    "/**\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, extractKeywords } from '../../utils/tieredIndex';\nimport type { FileSummary } from '../../domain/entities';\nimport { parsePathContext, formatPathContextForEmbedding } from '../../domain/services/keywords';\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    // Parse path context for structural awareness\n    const pathContext = parsePathContext(filepath);\n    const pathPrefix = formatPathContextForEmbedding(pathContext);\n\n    // Generate embeddings for all chunks with path context\n    // Prepending path context helps the embedding model understand file structure\n    const chunkContents = parsedChunks.map((c) => {\n      // For named chunks, include the name for better embedding\n      const namePrefix = c.name ? `${c.name}: ` : '';\n      return `${pathPrefix} ${namePrefix}${c.content}`;\n    });\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 + path keywords\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    // Add path keywords\n    pathContext.keywords.forEach(k => allKeywords.add(k));\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      // Include parsed path context for search boosting\n      pathContext: {\n        segments: pathContext.segments,\n        layer: pathContext.layer,\n        domain: pathContext.domain,\n        depth: pathContext.depth,\n      },\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    // Extract query terms for path matching\n    const queryTerms = query.toLowerCase().split(/\\s+/).filter(t => t.length > 2);\n    \n    // Build path boost map from file summaries\n    const pathBoosts = new Map<string, number>();\n    for (const filepath of candidateFiles) {\n      const summary = symbolicIndex.getFileSummary(filepath);\n      if (summary?.pathContext) {\n        let boost = 0;\n        const ctx = summary.pathContext;\n        \n        // Check if query terms match domain\n        if (ctx.domain && queryTerms.some(t => ctx.domain!.includes(t) || t.includes(ctx.domain!))) {\n          boost += 0.1;\n        }\n        \n        // Check if query terms match layer\n        if (ctx.layer && queryTerms.some(t => ctx.layer!.includes(t) || t.includes(ctx.layer!))) {\n          boost += 0.05;\n        }\n        \n        // Check if query terms match path segments\n        const segmentMatch = ctx.segments.some(seg => \n          queryTerms.some(t => seg.toLowerCase().includes(t) || t.includes(seg.toLowerCase()))\n        );\n        if (segmentMatch) {\n          boost += 0.05;\n        }\n        \n        pathBoosts.set(filepath, boost);\n      }\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      const pathBoost = pathBoosts.get(filepath) || 0;\n      \n      // Hybrid score: weighted combination of semantic, BM25, and path boost\n      const hybridScore = (SEMANTIC_WEIGHT * semanticScore) + (BM25_WEIGHT * bm25Score) + pathBoost;\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            pathBoost,\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",
+    "// 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\nexport interface IndexStatus {\n  /** Whether an index exists */\n  exists: boolean;\n  /** Root directory path */\n  rootDir: string;\n  /** Index directory path */\n  indexDir: string;\n  /** Last time the index was updated */\n  lastUpdated?: string;\n  /** Active modules and their file counts */\n  modules: Array<{\n    id: string;\n    fileCount: number;\n    lastUpdated: string;\n  }>;\n  /** Total number of indexed files */\n  totalFiles: 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\n/**\n * Get the current status of the index\n * @param rootDir - Root directory of the project\n * @returns Index status information\n */\nexport async function getIndexStatus(rootDir: string): Promise<IndexStatus> {\n  // Ensure absolute path\n  rootDir = path.resolve(rootDir);\n  \n  // Load config\n  const config = await loadConfig(rootDir);\n  const indexDir = path.join(rootDir, config.indexDir);\n  \n  const status: IndexStatus = {\n    exists: false,\n    rootDir,\n    indexDir,\n    modules: [],\n    totalFiles: 0,\n  };\n  \n  // Check if index directory exists\n  try {\n    await fs.access(indexDir);\n  } catch {\n    return status;\n  }\n  \n  // Try to load global manifest\n  try {\n    const globalManifestPath = getGlobalManifestPath(rootDir, config);\n    const content = await fs.readFile(globalManifestPath, 'utf-8');\n    const globalManifest: GlobalManifest = JSON.parse(content);\n    \n    status.exists = true;\n    status.lastUpdated = globalManifest.lastUpdated;\n    \n    // Load each module's manifest\n    for (const moduleId of globalManifest.modules) {\n      try {\n        const manifest = await loadModuleManifest(rootDir, moduleId, config);\n        const fileCount = Object.keys(manifest.files).length;\n        \n        status.modules.push({\n          id: moduleId,\n          fileCount,\n          lastUpdated: manifest.lastUpdated,\n        });\n        \n        status.totalFiles += fileCount;\n      } catch {\n        // Module manifest doesn't exist or is corrupt\n      }\n    }\n  } catch {\n    // Global manifest doesn't exist - check if there's any index data\n    try {\n      const entries = await fs.readdir(path.join(indexDir, 'index'));\n      if (entries.length > 0) {\n        status.exists = true;\n        // Try to load manifests for known modules\n        for (const entry of entries) {\n          try {\n            const manifest = await loadModuleManifest(rootDir, entry, config);\n            const fileCount = Object.keys(manifest.files).length;\n            \n            status.modules.push({\n              id: entry,\n              fileCount,\n              lastUpdated: manifest.lastUpdated,\n            });\n            \n            status.totalFiles += fileCount;\n          } catch {\n            // Skip\n          }\n        }\n      }\n    } catch {\n      // No index directory\n    }\n  }\n  \n  return status;\n}\n\n// Re-export watcher\nexport { watchDirectory, type WatchOptions, type FileWatcher } from './watcher';\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",
+    "/**\n * File watcher for incremental indexing\n * \n * Best practices implemented:\n * - Debouncing: Batches rapid file changes (e.g., IDE saves, git operations)\n * - Queuing: Prevents concurrent index operations\n * - Efficient filtering: Only watches relevant file types\n * - Graceful shutdown: Proper cleanup on SIGINT/SIGTERM\n * - Error recovery: Continues watching after index errors\n */\n\nimport { watch, type FSWatcher } from 'chokidar';\nimport * as path from 'path';\nimport { loadConfig } from '../utils/config';\nimport type { Config } from '../domain/entities';\nimport { indexDirectory, cleanupIndex, type IndexOptions, type IndexResult } from './index';\n\n/** Default debounce delay in milliseconds */\nconst DEFAULT_DEBOUNCE_MS = 300;\n\n/** Maximum files to batch before forcing an index */\nconst MAX_BATCH_SIZE = 100;\n\nexport interface WatchOptions extends IndexOptions {\n  /** Debounce delay in milliseconds (default: 300) */\n  debounceMs?: number;\n  /** Callback when indexing starts */\n  onIndexStart?: (files: string[]) => void;\n  /** Callback when indexing completes */\n  onIndexComplete?: (results: IndexResult[]) => void;\n  /** Callback when a file change is detected */\n  onFileChange?: (event: 'add' | 'change' | 'unlink', filepath: string) => void;\n  /** Callback for errors */\n  onError?: (error: Error) => void;\n}\n\nexport interface FileWatcher {\n  /** Stop watching and clean up */\n  stop: () => Promise<void>;\n  /** Whether the watcher is currently running */\n  isRunning: () => boolean;\n}\n\n/**\n * Start watching a directory for file changes and index incrementally\n */\nexport async function watchDirectory(\n  rootDir: string,\n  options: WatchOptions = {}\n): Promise<FileWatcher> {\n  const {\n    debounceMs = DEFAULT_DEBOUNCE_MS,\n    verbose = false,\n    model,\n    onIndexStart,\n    onIndexComplete,\n    onFileChange,\n    onError,\n  } = options;\n\n  // Ensure absolute path\n  rootDir = path.resolve(rootDir);\n  \n  // Load config\n  const config = await loadConfig(rootDir);\n  \n  // Build glob patterns for watched files\n  const watchPatterns = config.extensions.map(ext => `**/*${ext}`);\n  \n  // Build ignore patterns\n  const ignorePatterns = [\n    ...config.ignorePaths.map(p => `**/${p}/**`),\n    `**/${config.indexDir}/**`, // Always ignore the index directory\n  ];\n\n  // State management\n  let isRunning = true;\n  let isIndexing = false;\n  let pendingChanges = new Map<string, 'add' | 'change' | 'unlink'>();\n  let debounceTimer: ReturnType<typeof setTimeout> | null = null;\n  let watcher: FSWatcher | null = null;\n\n  /**\n   * Process pending file changes\n   */\n  async function processPendingChanges(): Promise<void> {\n    if (!isRunning || isIndexing || pendingChanges.size === 0) {\n      return;\n    }\n\n    isIndexing = true;\n    const changes = new Map(pendingChanges);\n    pendingChanges.clear();\n\n    try {\n      // Separate additions/changes from deletions\n      const filesToIndex: string[] = [];\n      const filesToDelete: string[] = [];\n\n      for (const [filepath, event] of changes) {\n        if (event === 'unlink') {\n          filesToDelete.push(filepath);\n        } else {\n          filesToIndex.push(filepath);\n        }\n      }\n\n      // Handle deletions via cleanup\n      if (filesToDelete.length > 0) {\n        if (verbose) {\n          console.log(`\\n[Watch] Cleaning up ${filesToDelete.length} deleted file(s)...`);\n        }\n        await cleanupIndex(rootDir, { verbose: false });\n      }\n\n      // Handle additions/changes via incremental index\n      if (filesToIndex.length > 0) {\n        if (onIndexStart) {\n          onIndexStart(filesToIndex);\n        }\n\n        if (verbose) {\n          console.log(`\\n[Watch] Indexing ${filesToIndex.length} changed file(s)...`);\n        }\n\n        const results = await indexDirectory(rootDir, {\n          model,\n          verbose: false, // Keep output clean in watch mode\n        });\n\n        if (onIndexComplete) {\n          onIndexComplete(results);\n        }\n\n        // Print summary\n        for (const result of results) {\n          if (result.indexed > 0 || result.errors > 0) {\n            console.log(`[Watch] ${result.moduleId}: ${result.indexed} indexed, ${result.errors} errors`);\n          }\n        }\n      }\n    } catch (error) {\n      const err = error instanceof Error ? error : new Error(String(error));\n      console.error('[Watch] Error during indexing:', err.message);\n      if (onError) {\n        onError(err);\n      }\n    } finally {\n      isIndexing = false;\n\n      // Process any changes that came in while we were indexing\n      if (pendingChanges.size > 0) {\n        scheduleProcessing();\n      }\n    }\n  }\n\n  /**\n   * Schedule processing of pending changes (with debounce)\n   */\n  function scheduleProcessing(): void {\n    if (debounceTimer) {\n      clearTimeout(debounceTimer);\n    }\n\n    // Force processing if batch is too large\n    if (pendingChanges.size >= MAX_BATCH_SIZE) {\n      processPendingChanges();\n      return;\n    }\n\n    debounceTimer = setTimeout(() => {\n      debounceTimer = null;\n      processPendingChanges();\n    }, debounceMs);\n  }\n\n  /**\n   * Handle a file event\n   */\n  function handleFileEvent(event: 'add' | 'change' | 'unlink', filepath: string): void {\n    if (!isRunning) return;\n\n    // Convert to relative path\n    const relativePath = path.relative(rootDir, filepath);\n\n    // Skip if it's in an ignored directory (extra safety check)\n    for (const ignorePath of config.ignorePaths) {\n      if (relativePath.startsWith(ignorePath) || relativePath.includes(`/${ignorePath}/`)) {\n        return;\n      }\n    }\n\n    if (onFileChange) {\n      onFileChange(event, relativePath);\n    }\n\n    if (verbose) {\n      const symbol = event === 'add' ? '+' : event === 'unlink' ? '-' : '~';\n      console.log(`[Watch] ${symbol} ${relativePath}`);\n    }\n\n    // Update pending changes (later events override earlier ones for same file)\n    pendingChanges.set(relativePath, event);\n    scheduleProcessing();\n  }\n\n  // Create the watcher\n  watcher = watch(watchPatterns, {\n    cwd: rootDir,\n    ignored: ignorePatterns,\n    persistent: true,\n    ignoreInitial: true, // Don't trigger events for existing files\n    awaitWriteFinish: {\n      stabilityThreshold: 100, // Wait for file to be stable\n      pollInterval: 50,\n    },\n    // Performance optimizations\n    usePolling: false, // Use native fs events when possible\n    atomic: true, // Handle atomic writes (common in editors)\n  });\n\n  // Set up event handlers\n  watcher.on('add', (filepath) => handleFileEvent('add', path.join(rootDir, filepath)));\n  watcher.on('change', (filepath) => handleFileEvent('change', path.join(rootDir, filepath)));\n  watcher.on('unlink', (filepath) => handleFileEvent('unlink', path.join(rootDir, filepath)));\n\n  watcher.on('error', (error: unknown) => {\n    const err = error instanceof Error ? error : new Error(String(error));\n    console.error('[Watch] Watcher error:', err);\n    if (onError) {\n      onError(err);\n    }\n  });\n\n  // Wait for watcher to be ready\n  await new Promise<void>((resolve) => {\n    watcher!.on('ready', () => {\n      resolve();\n    });\n  });\n\n  // Return control interface\n  return {\n    stop: async () => {\n      isRunning = false;\n      \n      if (debounceTimer) {\n        clearTimeout(debounceTimer);\n        debounceTimer = null;\n      }\n      \n      if (watcher) {\n        await watcher.close();\n        watcher = null;\n      }\n    },\n    isRunning: () => isRunning,\n  };\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",
     "/**\n * RAGgrep - Local filesystem-based RAG system for codebases\n * \n * Provides semantic search over code using local embeddings.\n * \n * @example\n * ```ts\n * import raggrep from 'raggrep';\n * \n * // Index a directory\n * await raggrep.index('/path/to/project');\n * \n * // Search the index\n * const results = await raggrep.search('/path/to/project', 'user authentication');\n * \n * // Clean up stale entries\n * await raggrep.cleanup('/path/to/project');\n * ```\n */\n\nimport { indexDirectory, cleanupIndex } from './indexer';\nimport type { IndexResult, IndexOptions, CleanupResult } from './indexer';\nimport { search as searchIndex, formatSearchResults } from './search';\nimport type { SearchOptions, SearchResult } from './types';\n\n// Re-export types\nexport type { IndexResult, IndexOptions, CleanupResult } from './indexer';\nexport type { SearchOptions, SearchResult, Chunk, FileIndex } from './types';\n\n/**\n * Index a directory for semantic search.\n * \n * Creates a `.raggrep/` folder with the index data.\n * \n * @param directory - Path to the directory to index\n * @param options - Index options\n * @returns Array of results per module\n * \n * @example\n * ```ts\n * // Basic indexing\n * await raggrep.index('./my-project');\n * \n * // With options\n * await raggrep.index('./my-project', {\n *   model: 'bge-small-en-v1.5',\n *   verbose: true\n * });\n * ```\n */\nexport async function index(\n  directory: string, \n  options: IndexOptions = {}\n): Promise<IndexResult[]> {\n  return indexDirectory(directory, options);\n}\n\n/**\n * Search the indexed codebase.\n * \n * @param directory - Path to the indexed directory\n * @param query - Natural language search query\n * @param options - Search options\n * @returns Array of search results sorted by relevance\n * \n * @example\n * ```ts\n * // Basic search\n * const results = await raggrep.search('./my-project', 'user login');\n * \n * // With options\n * const results = await raggrep.search('./my-project', 'database query', {\n *   topK: 5,\n *   minScore: 0.2,\n *   filePatterns: ['*.ts']\n * });\n * ```\n */\nexport async function search(\n  directory: string,\n  query: string,\n  options: SearchOptions = {}\n): Promise<SearchResult[]> {\n  return searchIndex(directory, query, options);\n}\n\n/**\n * Clean up stale index entries for files that no longer exist.\n * \n * @param directory - Path to the indexed directory\n * @param options - Cleanup options\n * @returns Array of cleanup results per module\n * \n * @example\n * ```ts\n * const results = await raggrep.cleanup('./my-project');\n * console.log(`Removed ${results[0].removed} stale entries`);\n * ```\n */\nexport async function cleanup(\n  directory: string,\n  options: { verbose?: boolean } = {}\n): Promise<CleanupResult[]> {\n  return cleanupIndex(directory, options);\n}\n\n/**\n * Format search results for display.\n * \n * @param results - Array of search results\n * @returns Formatted string for console output\n */\nexport { formatSearchResults };\n\n// Default export for convenient importing\nconst raggrep = {\n  index,\n  search,\n  cleanup,\n  formatSearchResults,\n};\n\nexport default raggrep;\n\n"
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+  "debugId": "791A08B2C54816DA64756E2164756E21",
   "names": []
 }

package/dist/indexer/index.d.ts

@@ -18,6 +18,24 @@ export interface CleanupResult {
     /** Number of valid entries kept */
     kept: number;
 }
+export interface IndexStatus {
+    /** Whether an index exists */
+    exists: boolean;
+    /** Root directory path */
+    rootDir: string;
+    /** Index directory path */
+    indexDir: string;
+    /** Last time the index was updated */
+    lastUpdated?: string;
+    /** Active modules and their file counts */
+    modules: Array<{
+        id: string;
+        fileCount: number;
+        lastUpdated: string;
+    }>;
+    /** Total number of indexed files */
+    totalFiles: number;
+}
 /**
  * Index a directory using all enabled modules
  */
@@ -31,3 +49,10 @@ export declare function indexDirectory(rootDir: string, options?: IndexOptions):
 export declare function cleanupIndex(rootDir: string, options?: {
     verbose?: boolean;
 }): Promise<CleanupResult[]>;
+/**
+ * Get the current status of the index
+ * @param rootDir - Root directory of the project
+ * @returns Index status information
+ */
+export declare function getIndexStatus(rootDir: string): Promise<IndexStatus>;
+export { watchDirectory, type WatchOptions, type FileWatcher } from './watcher';

package/dist/indexer/watcher.d.ts

@@ -0,0 +1,33 @@
+/**
+ * File watcher for incremental indexing
+ *
+ * Best practices implemented:
+ * - Debouncing: Batches rapid file changes (e.g., IDE saves, git operations)
+ * - Queuing: Prevents concurrent index operations
+ * - Efficient filtering: Only watches relevant file types
+ * - Graceful shutdown: Proper cleanup on SIGINT/SIGTERM
+ * - Error recovery: Continues watching after index errors
+ */
+import { type IndexOptions, type IndexResult } from './index';
+export interface WatchOptions extends IndexOptions {
+    /** Debounce delay in milliseconds (default: 300) */
+    debounceMs?: number;
+    /** Callback when indexing starts */
+    onIndexStart?: (files: string[]) => void;
+    /** Callback when indexing completes */
+    onIndexComplete?: (results: IndexResult[]) => void;
+    /** Callback when a file change is detected */
+    onFileChange?: (event: 'add' | 'change' | 'unlink', filepath: string) => void;
+    /** Callback for errors */
+    onError?: (error: Error) => void;
+}
+export interface FileWatcher {
+    /** Stop watching and clean up */
+    stop: () => Promise<void>;
+    /** Whether the watcher is currently running */
+    isRunning: () => boolean;
+}
+/**
+ * Start watching a directory for file changes and index incrementally
+ */
+export declare function watchDirectory(rootDir: string, options?: WatchOptions): Promise<FileWatcher>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "raggrep",
-  "version": "0.1.0",
+  "version": "0.1.3",
   "description": "Local filesystem-based RAG system for codebases - semantic search using local embeddings",
   "type": "module",
   "main": "./dist/index.js",
@@ -22,9 +22,9 @@
   "scripts": {
     "build": "bun run build:clean && bun run build:bundle && bun run build:types && bun run build:shebang",
     "build:clean": "rm -rf dist",
-    "build:bundle": "bun build src/index.ts --outdir dist --target node --sourcemap=external --external '@xenova/transformers' --external 'glob' --external 'typescript' && bun build src/cli/main.ts --outdir dist/cli --target node --sourcemap=external --external '@xenova/transformers' --external 'glob' --external 'typescript'",
+    "build:bundle": "bun build src/index.ts --outdir dist --target node --sourcemap=external --external '@xenova/transformers' --external 'glob' --external 'typescript' --external 'chokidar' && bun build src/cli/main.ts --outdir dist/cli --target node --sourcemap=external --external '@xenova/transformers' --external 'glob' --external 'typescript' --external 'chokidar'",
     "build:types": "tsc --emitDeclarationOnly --outDir dist",
-    "build:shebang": "echo '#!/usr/bin/env node' | cat - dist/cli/main.js > temp && mv temp dist/cli/main.js",
+    "build:shebang": "echo '#!/usr/bin/env node' | cat - dist/cli/main.js > temp && mv temp dist/cli/main.js && chmod +x dist/cli/main.js",
     "prepublishOnly": "bun run build",
     "raggrep": "bun run src/cli/main.ts",
     "test": "bun test",
@@ -56,6 +56,7 @@
   },
   "dependencies": {
     "@xenova/transformers": "^2.17.0",
+    "chokidar": "^5.0.0",
     "glob": "^10.0.0",
     "typescript": "^5.0.0"
   },