kirograph 0.20.0 → 0.22.0

package/dist/config.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../src/config.ts"],
-  "sourcesContent": ["/**\n * KiroGraph Config System\n *\n * Mirrors CodeGraph src/config.ts \u2014 load, save, validate, and provide defaults\n * for KiroGraph configuration.\n */\n\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport picomatch from 'picomatch';\nimport { logWarn, logError } from './errors';\n\n// \u2500\u2500 Types \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport interface KiroGraphConfig {\n  version: number;\n  languages: string[];\n  include: string[];\n  exclude: string[];\n  maxFileSize: number;\n  extractDocstrings: boolean;\n  trackCallSites: boolean;\n  // Parity fields:\n  enableEmbeddings: boolean;\n  embeddingModel: string;\n  embeddingDim: number;\n  /** @deprecated Use semanticEngine instead. Kept for backwards compatibility. */\n  useVecIndex: boolean;\n  semanticEngine: 'cosine' | 'sqlite-vec' | 'orama' | 'pglite' | 'lancedb' | 'qdrant' | 'typesense';\n  typesenseDashboard: boolean;\n  qdrantDashboard: boolean;\n  minLogLevel: 'debug' | 'info' | 'warn' | 'error';\n  frameworkHints: string[];\n  fuzzyResolutionThreshold: number; // 0.0\u20131.0\n  /** Enable architecture analysis (package graph + layer detection). Default: false. */\n  enableArchitecture: boolean;\n  /**\n   * User-defined layer \u2192 glob pattern overrides.\n   * When set, config-defined layers win over auto-detected ones.\n   * Example: { \"api\": [\"src/routes/**\", \"src/controllers/**\"] }\n   */\n  architectureLayers?: Record<string, string[]>;\n  /** Agent communication style injected at agentSpawn. Default: 'off'. */\n  cavemanMode: 'off' | 'lite' | 'full' | 'ultra';\n  /** Shell compression level for kirograph_exec. 'off' disables the hook/steering. Default: 'normal'. */\n  shellCompressionLevel: 'off' | 'normal' | 'aggressive' | 'ultra';\n  /**\n   * Number of pending (unindexed) files above which kirograph_status warns the agent.\n   * Set to 0 to disable the warning. Default: 10.\n   */\n  syncWarningThreshold: number;\n  /** Enable persistent cross-session memory. Default: false. */\n  enableMemory: boolean;\n  /** FTS/vector blend for memory search: 0 = FTS only, 1 = vector only. Default: 0.5. */\n  memorySearchAlpha: number;\n  /** Store uncompressed originals when caveman is on. Default: false. */\n  memoryKeepRaw: boolean;\n  /** Auto-prune threshold (max observations). 0 = no limit. Default: 10000. */\n  memoryMaxObservations: number;\n  /** Seconds of inactivity before auto-closing a session. Default: 7200. */\n  memorySessionTimeout: number;\n  /** Max observations shown in kirograph_context. Default: 3. */\n  memoryContextLimit: number;\n  /** Min relevance score to include memory in context. Default: 0.3. */\n  memoryContextThreshold: number;\n  /** Glob patterns for paths to never capture in memory. Default: []. */\n  memoryExcludePatterns: string[];\n  /** Enable watchmen \u2014 auto-synthesize workspace briefs from memory observations. Requires enableMemory. Default: false. */\n  enableWatchmen: boolean;\n  /** Minimum new observations since last synthesis before watchmenReady fires. Default: 5. */\n  watchmenThreshold: number;\n  /**\n   * How synthesis is performed.\n   * 'local' \u2014 runs a local HuggingFace model via @huggingface/transformers (no API cost, works for all tools).\n   * 'agent' \u2014 delegates to the active AI agent via askAgent hook (Kiro only, consumes agent tokens).\n   * Default: 'local'.\n   */\n  watchmenSynthesisMode: 'local' | 'agent';\n  /** HuggingFace model ID for local synthesis. Only used when watchmenSynthesisMode is 'local'. Default: 'onnx-community/gemma-4-E4B-it-ONNX'. */\n  watchmenLocalModel: string;\n  /** Enable documentation indexing and navigation. Default: false. */\n  enableDocs: boolean;\n  /** Glob patterns for documentation files to include. */\n  docsInclude: string[];\n  /** Glob patterns for documentation files to exclude. */\n  docsExclude: string[];\n  /** Enable auto-linking of doc sections to code symbols. Default: true. */\n  docsLinkCode: boolean;\n  /** Max doc sections to include in kirograph_context. 0 = disabled. Default: 0. */\n  docsContextLimit: number;\n  /** Min relevance score to include a doc section in context. Default: 0.3. */\n  docsContextThreshold: number;\n  /** Max file size for doc files (bytes). Default: 1MB. */\n  docsMaxFileSize: number;\n  /** Summarization strategy. Default: 'first-sentence'. */\n  docsSummarization: 'embedding' | 'first-sentence' | 'off';\n  /** Enable tabular data indexing and querying. Default: false. */\n  enableData: boolean;\n  /** Glob patterns for data files to include. */\n  dataInclude: string[];\n  /** Glob patterns for data files to exclude. */\n  dataExclude: string[];\n  /** Enable auto-linking of data files to code symbols. Default: true. */\n  dataLinkCode: boolean;\n  /** Max datasets to include in kirograph_context. 0 = disabled. Default: 0. */\n  dataContextLimit: number;\n  /** Max file size for data files (bytes). Default: 50MB. */\n  dataMaxFileSize: number;\n  /** Max rows to index per file. Default: 1,000,000. */\n  dataMaxRows: number;\n  /** Max rows returned per query. Default: 500. */\n  dataQueryLimit: number;\n  /** Max token budget per response. Default: 8000. */\n  dataMaxResponseTokens: number;\n  /** Enable security analysis (dependency scanning + vulnerability detection). Default: false. */\n  enableSecurity: boolean;\n  /** Vulnerability databases to query. Default: ['OSV']. */\n  securityDatabases: string[];\n  /** Enable AST-level structural pattern matching (SAST) during indexing. Default: false. */\n  enablePatterns: boolean;\n  /** Path to a directory of user-supplied YAML rule files. Merged with bundled library (user rules win on id conflict). Default: undefined. */\n  patternLibraryPath: string | undefined;\n  /** Minimum severity level for storing pattern matches during index-time analysis. Default: 'low'. */\n  patternSeverityThreshold: 'critical' | 'high' | 'medium' | 'low';\n  /** Auto-run vulnerability enrichment after manifest parsing. Default: true. */\n  securityAutoEnrich: boolean;\n  /** Max age in days for vulnerability data before showing a staleness warning. Default: 7. */\n  securityEnrichMaxAgeDays: number;\n  /**\n   * License policy for dependency compliance.\n   * deny: licenses to block (build fails / command exits non-zero).\n   * warn: licenses to flag as warnings.\n   * Patterns support wildcards: GPL-* matches GPL-2.0, GPL-3.0, etc.\n   * Default: { deny: [], warn: [] }.\n   */\n  securityLicensePolicy: {\n    deny: string[];\n    warn: string[];\n  };\n  /** Context budget governance settings. */\n  contextBudget?: {\n    maxTokensPerSession: number;\n    warnAt: number;\n    throttleAt: number;\n  };\n}\n\n// \u2500\u2500 Constants \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nconst KIROGRAPH_DIR = '.kirograph';\nconst CONFIG_FILE = 'config.json';\n\nconst KNOWN_FIELDS = new Set<string>([\n  'version', 'languages', 'include', 'exclude', 'maxFileSize',\n  'extractDocstrings', 'trackCallSites', 'enableEmbeddings', 'embeddingModel', 'embeddingDim',\n  'useVecIndex', 'semanticEngine', 'typesenseDashboard', 'qdrantDashboard',\n  'minLogLevel', 'frameworkHints', 'fuzzyResolutionThreshold',\n  'enableArchitecture', 'architectureLayers', 'cavemanMode', 'shellCompressionLevel', 'syncWarningThreshold',\n  'enableMemory', 'memorySearchAlpha', 'memoryKeepRaw', 'memoryMaxObservations',\n  'memorySessionTimeout', 'memoryContextLimit', 'memoryContextThreshold', 'memoryExcludePatterns',\n  'enableWatchmen', 'watchmenThreshold', 'watchmenSynthesisMode', 'watchmenLocalModel',\n  'enableDocs', 'docsInclude', 'docsExclude', 'docsLinkCode',\n  'docsContextLimit', 'docsContextThreshold', 'docsMaxFileSize', 'docsSummarization',\n  'enableData', 'dataInclude', 'dataExclude', 'dataLinkCode',\n  'dataContextLimit', 'dataMaxFileSize', 'dataMaxRows', 'dataQueryLimit', 'dataMaxResponseTokens',\n  'enableSecurity', 'securityDatabases', 'securityAutoEnrich', 'securityEnrichMaxAgeDays', 'securityLicensePolicy',\n  'enablePatterns', 'patternLibraryPath', 'patternSeverityThreshold',\n  'contextBudget',\n  // Legacy aliases (still accepted, mapped during validation)\n  'enableCompression', 'compressionLevel',\n]);\n\nconst LOG_LEVELS = new Set(['debug', 'info', 'warn', 'error']);\n\n// \u2500\u2500 ReDoS-safe regex check \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Returns false if the pattern is potentially dangerous (ReDoS risk) or too long.\n * Checks for catastrophic backtracking patterns like (a+)+ or (a|a)+.\n */\nexport function isSafeRegex(pattern: string): boolean {\n  if (pattern.length > 100) return false;\n  // Detect nested quantifiers: (x+)+ or (x*)+ or (x+)* etc.\n  if (/\\([^)]*[+*][^)]*\\)[+*?]/.test(pattern)) return false;\n  // Detect alternation with overlap: (a|a)+ style\n  if (/\\([^)]*\\|[^)]*\\)[+*]/.test(pattern)) return false;\n  return true;\n}\n\n// \u2500\u2500 Default config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport function createDefaultConfig(_projectRoot?: string): KiroGraphConfig {\n  return {\n    version: 2,\n    languages: [],\n    include: [],\n    exclude: ['**/node_modules/**', '**/dist/**', '**/build/**', '**/.git/**', '*.min.js', '**/.kirograph/**'],\n    maxFileSize: 1_048_576,\n    extractDocstrings: true,\n    trackCallSites: true,\n    enableEmbeddings: false,\n    embeddingModel: 'nomic-ai/nomic-embed-text-v1.5',\n    embeddingDim: 768,\n    useVecIndex: false,\n    semanticEngine: 'cosine',\n    typesenseDashboard: false,\n    qdrantDashboard: false,\n    minLogLevel: 'warn',\n    frameworkHints: [],\n    fuzzyResolutionThreshold: 0.5,\n    enableArchitecture: false,\n    cavemanMode: 'off',\n    shellCompressionLevel: 'normal',\n    syncWarningThreshold: 10,\n    enableMemory: false,\n    memorySearchAlpha: 0.5,\n    memoryKeepRaw: false,\n    memoryMaxObservations: 10000,\n    memorySessionTimeout: 7200,\n    memoryContextLimit: 3,\n    memoryContextThreshold: 0.3,\n    memoryExcludePatterns: [],\n    enableWatchmen: false,\n    watchmenThreshold: 5,\n    watchmenSynthesisMode: 'local',\n    watchmenLocalModel: 'onnx-community/gemma-4-E4B-it-ONNX',\n    enableDocs: false,\n    docsInclude: ['**/*.md', '**/*.mdx', '**/*.rst', '**/*.adoc', '**/*.asciidoc', '**/*.rdoc', '**/*.org', '**/*.cheatmd', 'docs/**/*.txt', 'docs/**/*.html'],\n    docsExclude: ['node_modules/**', '**/CHANGELOG*', '**/LICENSE*', '**/CHANGES*', 'dist/**', 'build/**', 'coverage/**', '.git/**', '**/generated/**', '**/auto-generated/**', '**/vendor/**', '_build/**'],\n    docsLinkCode: true,\n    docsContextLimit: 0,\n    docsContextThreshold: 0.3,\n    docsMaxFileSize: 1_048_576,\n    docsSummarization: 'first-sentence',\n    enableData: false,\n    dataInclude: ['**/*.csv', '**/*.tsv', '**/*.jsonl', '**/*.ndjson', '**/*.xlsx', '**/*.xls', '**/*.parquet', 'data/**/*.json'],\n    dataExclude: ['node_modules/**', 'dist/**', 'build/**', '.git/**', '**/package-lock.json', '**/yarn.lock', '**/pnpm-lock.yaml', '**/tsconfig.json', '**/jsconfig.json', 'coverage/**', '**/generated/**'],\n    dataLinkCode: true,\n    dataContextLimit: 0,\n    dataMaxFileSize: 52_428_800,\n    dataMaxRows: 1_000_000,\n    dataQueryLimit: 500,\n    dataMaxResponseTokens: 8000,\n    enableSecurity: false,\n    securityDatabases: ['OSV'],\n    securityAutoEnrich: true,\n    securityEnrichMaxAgeDays: 7,\n    securityLicensePolicy: { deny: [], warn: [] },\n    enablePatterns: false,\n    patternLibraryPath: undefined,\n    patternSeverityThreshold: 'low',\n  };\n}\n\n// \u2500\u2500 Validation \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport function validateConfig(config: unknown): KiroGraphConfig {\n  const defaults = createDefaultConfig();\n\n  if (typeof config !== 'object' || config === null) {\n    return defaults;\n  }\n\n  const raw = config as Record<string, unknown>;\n\n  // Warn about unknown fields\n  for (const key of Object.keys(raw)) {\n    if (!KNOWN_FIELDS.has(key)) {\n      logWarn(`Unknown config field: ${key}`);\n    }\n  }\n\n  // Validate and coerce each field\n  const version = typeof raw.version === 'number' ? raw.version : defaults.version;\n  const languages = Array.isArray(raw.languages) && raw.languages.every(l => typeof l === 'string')\n    ? (raw.languages as string[])\n    : defaults.languages;\n  const maxFileSize = typeof raw.maxFileSize === 'number' && raw.maxFileSize > 0\n    ? raw.maxFileSize\n    : defaults.maxFileSize;\n  const extractDocstrings = typeof raw.extractDocstrings === 'boolean'\n    ? raw.extractDocstrings\n    : defaults.extractDocstrings;\n  const trackCallSites = typeof raw.trackCallSites === 'boolean'\n    ? raw.trackCallSites\n    : defaults.trackCallSites;\n  const enableEmbeddings = typeof raw.enableEmbeddings === 'boolean'\n    ? raw.enableEmbeddings\n    : defaults.enableEmbeddings;\n  const embeddingModel = typeof raw.embeddingModel === 'string' && raw.embeddingModel.length > 0\n    ? raw.embeddingModel\n    : defaults.embeddingModel;\n  const embeddingDim = typeof raw.embeddingDim === 'number' && raw.embeddingDim > 0\n    ? raw.embeddingDim\n    : defaults.embeddingDim;\n  const useVecIndex = typeof raw.useVecIndex === 'boolean'\n    ? raw.useVecIndex\n    : defaults.useVecIndex;\n  const SEMANTIC_ENGINES = new Set(['cosine', 'sqlite-vec', 'orama', 'pglite', 'lancedb', 'qdrant', 'typesense']);\n  // useVecIndex is a legacy alias: if set and no explicit semanticEngine, map it\n  const semanticEngine = typeof raw.semanticEngine === 'string' && SEMANTIC_ENGINES.has(raw.semanticEngine)\n    ? (raw.semanticEngine as KiroGraphConfig['semanticEngine'])\n    : useVecIndex ? 'sqlite-vec' : defaults.semanticEngine;\n  const typesenseDashboard = typeof raw.typesenseDashboard === 'boolean'\n    ? raw.typesenseDashboard\n    : defaults.typesenseDashboard;\n  const qdrantDashboard = typeof raw.qdrantDashboard === 'boolean'\n    ? raw.qdrantDashboard\n    : defaults.qdrantDashboard;\n  const minLogLevel = typeof raw.minLogLevel === 'string' && LOG_LEVELS.has(raw.minLogLevel)\n    ? (raw.minLogLevel as KiroGraphConfig['minLogLevel'])\n    : defaults.minLogLevel;\n  const frameworkHints = Array.isArray(raw.frameworkHints) && raw.frameworkHints.every(h => typeof h === 'string')\n    ? (raw.frameworkHints as string[])\n    : defaults.frameworkHints;\n  const fuzzyResolutionThreshold = typeof raw.fuzzyResolutionThreshold === 'number'\n    && raw.fuzzyResolutionThreshold >= 0\n    && raw.fuzzyResolutionThreshold <= 1\n    ? raw.fuzzyResolutionThreshold\n    : defaults.fuzzyResolutionThreshold;\n  const enableArchitecture = typeof raw.enableArchitecture === 'boolean'\n    ? raw.enableArchitecture\n    : defaults.enableArchitecture;\n  const architectureLayers = _validateArchitectureLayers(raw.architectureLayers);\n  const CAVEMAN_MODES = new Set(['off', 'lite', 'full', 'ultra']);\n  const cavemanMode = typeof raw.cavemanMode === 'string' && CAVEMAN_MODES.has(raw.cavemanMode)\n    ? (raw.cavemanMode as KiroGraphConfig['cavemanMode'])\n    : defaults.cavemanMode;\n  const COMPRESSION_LEVELS = new Set(['off', 'normal', 'aggressive', 'ultra']);\n  // Support legacy field names: enableCompression (boolean) and compressionLevel (string)\n  let shellCompressionLevel: KiroGraphConfig['shellCompressionLevel'];\n  if (typeof raw.shellCompressionLevel === 'string' && COMPRESSION_LEVELS.has(raw.shellCompressionLevel)) {\n    shellCompressionLevel = raw.shellCompressionLevel as KiroGraphConfig['shellCompressionLevel'];\n  } else if (typeof raw.compressionLevel === 'string' && COMPRESSION_LEVELS.has(raw.compressionLevel)) {\n    shellCompressionLevel = raw.compressionLevel as KiroGraphConfig['shellCompressionLevel'];\n  } else if (typeof raw.enableCompression === 'boolean') {\n    shellCompressionLevel = raw.enableCompression ? 'normal' : 'off';\n  } else {\n    shellCompressionLevel = defaults.shellCompressionLevel;\n  }\n  const syncWarningThreshold = typeof raw.syncWarningThreshold === 'number' && raw.syncWarningThreshold >= 0\n    ? Math.round(raw.syncWarningThreshold)\n    : defaults.syncWarningThreshold;\n\n  // \u2500\u2500 Memory config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const enableMemory = typeof raw.enableMemory === 'boolean'\n    ? raw.enableMemory\n    : defaults.enableMemory;\n  const memorySearchAlpha = typeof raw.memorySearchAlpha === 'number'\n    && raw.memorySearchAlpha >= 0 && raw.memorySearchAlpha <= 1\n    ? raw.memorySearchAlpha\n    : defaults.memorySearchAlpha;\n  const memoryKeepRaw = typeof raw.memoryKeepRaw === 'boolean'\n    ? raw.memoryKeepRaw\n    : defaults.memoryKeepRaw;\n  const memoryMaxObservations = typeof raw.memoryMaxObservations === 'number' && raw.memoryMaxObservations >= 0\n    ? Math.round(raw.memoryMaxObservations)\n    : defaults.memoryMaxObservations;\n  const memorySessionTimeout = typeof raw.memorySessionTimeout === 'number' && raw.memorySessionTimeout > 0\n    ? Math.round(raw.memorySessionTimeout)\n    : defaults.memorySessionTimeout;\n  const memoryContextLimit = typeof raw.memoryContextLimit === 'number' && raw.memoryContextLimit >= 0\n    ? Math.round(raw.memoryContextLimit)\n    : defaults.memoryContextLimit;\n  const memoryContextThreshold = typeof raw.memoryContextThreshold === 'number'\n    && raw.memoryContextThreshold >= 0 && raw.memoryContextThreshold <= 1\n    ? raw.memoryContextThreshold\n    : defaults.memoryContextThreshold;\n  const memoryExcludePatterns = Array.isArray(raw.memoryExcludePatterns)\n    && raw.memoryExcludePatterns.every((p: unknown) => typeof p === 'string')\n    ? (raw.memoryExcludePatterns as string[])\n    : defaults.memoryExcludePatterns;\n\n  // \u2500\u2500 Watchmen config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const enableWatchmen = typeof raw.enableWatchmen === 'boolean'\n    ? raw.enableWatchmen\n    : defaults.enableWatchmen;\n  const watchmenThreshold = typeof raw.watchmenThreshold === 'number' && raw.watchmenThreshold > 0\n    ? Math.round(raw.watchmenThreshold)\n    : defaults.watchmenThreshold;\n  const WATCHMEN_SYNTHESIS_MODES = new Set(['local', 'agent']);\n  const watchmenSynthesisMode = typeof raw.watchmenSynthesisMode === 'string' && WATCHMEN_SYNTHESIS_MODES.has(raw.watchmenSynthesisMode)\n    ? (raw.watchmenSynthesisMode as KiroGraphConfig['watchmenSynthesisMode'])\n    : defaults.watchmenSynthesisMode;\n  const watchmenLocalModel = typeof raw.watchmenLocalModel === 'string' && raw.watchmenLocalModel.length > 0\n    ? raw.watchmenLocalModel\n    : defaults.watchmenLocalModel;\n\n  // \u2500\u2500 Docs config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const enableDocs = typeof raw.enableDocs === 'boolean'\n    ? raw.enableDocs\n    : defaults.enableDocs;\n  const docsInclude = Array.isArray(raw.docsInclude)\n    && raw.docsInclude.every((p: unknown) => typeof p === 'string')\n    ? (raw.docsInclude as string[])\n    : defaults.docsInclude;\n  const docsExclude = Array.isArray(raw.docsExclude)\n    && raw.docsExclude.every((p: unknown) => typeof p === 'string')\n    ? (raw.docsExclude as string[])\n    : defaults.docsExclude;\n  const docsLinkCode = typeof raw.docsLinkCode === 'boolean'\n    ? raw.docsLinkCode\n    : defaults.docsLinkCode;\n  const docsContextLimit = typeof raw.docsContextLimit === 'number' && raw.docsContextLimit >= 0\n    ? Math.round(raw.docsContextLimit)\n    : defaults.docsContextLimit;\n  const docsContextThreshold = typeof raw.docsContextThreshold === 'number'\n    && raw.docsContextThreshold >= 0 && raw.docsContextThreshold <= 1\n    ? raw.docsContextThreshold\n    : defaults.docsContextThreshold;\n  const docsMaxFileSize = typeof raw.docsMaxFileSize === 'number' && raw.docsMaxFileSize > 0\n    ? raw.docsMaxFileSize\n    : defaults.docsMaxFileSize;\n  const DOCS_SUMMARIZATION_MODES = new Set(['embedding', 'first-sentence', 'off']);\n  const docsSummarization = typeof raw.docsSummarization === 'string' && DOCS_SUMMARIZATION_MODES.has(raw.docsSummarization)\n    ? (raw.docsSummarization as KiroGraphConfig['docsSummarization'])\n    : defaults.docsSummarization;\n\n  // \u2500\u2500 Data config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const enableData = typeof raw.enableData === 'boolean' ? raw.enableData : defaults.enableData;\n  const dataInclude = Array.isArray(raw.dataInclude) && raw.dataInclude.every((p: unknown) => typeof p === 'string')\n    ? (raw.dataInclude as string[]) : defaults.dataInclude;\n  const dataExclude = Array.isArray(raw.dataExclude) && raw.dataExclude.every((p: unknown) => typeof p === 'string')\n    ? (raw.dataExclude as string[]) : defaults.dataExclude;\n  const dataLinkCode = typeof raw.dataLinkCode === 'boolean' ? raw.dataLinkCode : defaults.dataLinkCode;\n  const dataContextLimit = typeof raw.dataContextLimit === 'number' && raw.dataContextLimit >= 0\n    ? Math.round(raw.dataContextLimit) : defaults.dataContextLimit;\n  const dataMaxFileSize = typeof raw.dataMaxFileSize === 'number' && raw.dataMaxFileSize > 0\n    ? raw.dataMaxFileSize : defaults.dataMaxFileSize;\n  const dataMaxRows = typeof raw.dataMaxRows === 'number' && raw.dataMaxRows > 0\n    ? Math.round(raw.dataMaxRows) : defaults.dataMaxRows;\n  const dataQueryLimit = typeof raw.dataQueryLimit === 'number' && raw.dataQueryLimit > 0\n    ? Math.min(Math.round(raw.dataQueryLimit), 500) : defaults.dataQueryLimit;\n  const dataMaxResponseTokens = typeof raw.dataMaxResponseTokens === 'number' && raw.dataMaxResponseTokens > 0\n    ? Math.round(raw.dataMaxResponseTokens) : defaults.dataMaxResponseTokens;\n\n  // \u2500\u2500 Security config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let enableSecurity: boolean;\n  if (typeof raw.enableSecurity === 'boolean') {\n    enableSecurity = raw.enableSecurity;\n  } else {\n    if (raw.enableSecurity !== undefined) {\n      logWarn('Invalid config field enableSecurity: expected boolean, applying default (false)');\n    }\n    enableSecurity = defaults.enableSecurity;\n  }\n\n  let securityAutoEnrich: boolean;\n  if (typeof raw.securityAutoEnrich === 'boolean') {\n    securityAutoEnrich = raw.securityAutoEnrich;\n  } else {\n    if (raw.securityAutoEnrich !== undefined) {\n      logWarn('Invalid config field securityAutoEnrich: expected boolean, applying default (true)');\n    }\n    securityAutoEnrich = defaults.securityAutoEnrich;\n  }\n\n  let securityEnrichMaxAgeDays: number;\n  if (typeof raw.securityEnrichMaxAgeDays === 'number' && raw.securityEnrichMaxAgeDays > 0) {\n    securityEnrichMaxAgeDays = raw.securityEnrichMaxAgeDays;\n  } else {\n    if (raw.securityEnrichMaxAgeDays !== undefined) {\n      logWarn('Invalid config field securityEnrichMaxAgeDays: expected positive number, applying default (7)');\n    }\n    securityEnrichMaxAgeDays = defaults.securityEnrichMaxAgeDays;\n  }\n\n  const SUPPORTED_SECURITY_DATABASES = new Set(['OSV']);\n  let securityDatabases: string[];\n  if (Array.isArray(raw.securityDatabases) && raw.securityDatabases.every((d: unknown) => typeof d === 'string')) {\n    const valid = (raw.securityDatabases as string[]).filter(d => {\n      if (!SUPPORTED_SECURITY_DATABASES.has(d)) {\n        logWarn(`Unsupported security database \"${d}\" in securityDatabases, ignoring`);\n        return false;\n      }\n      return true;\n    });\n    securityDatabases = valid.length > 0 ? valid : defaults.securityDatabases;\n  } else {\n    if (raw.securityDatabases !== undefined) {\n      logWarn('Invalid config field securityDatabases: expected array of strings, applying default ([\"OSV\"])');\n    }\n    securityDatabases = defaults.securityDatabases;\n  }\n\n  let securityLicensePolicy: KiroGraphConfig['securityLicensePolicy'];\n  if (raw.securityLicensePolicy && typeof raw.securityLicensePolicy === 'object' && !Array.isArray(raw.securityLicensePolicy)) {\n    const rawPolicy = raw.securityLicensePolicy as Record<string, unknown>;\n    const deny = Array.isArray(rawPolicy.deny) && rawPolicy.deny.every((p: unknown) => typeof p === 'string')\n      ? (rawPolicy.deny as string[])\n      : defaults.securityLicensePolicy.deny;\n    const warn = Array.isArray(rawPolicy.warn) && rawPolicy.warn.every((p: unknown) => typeof p === 'string')\n      ? (rawPolicy.warn as string[])\n      : defaults.securityLicensePolicy.warn;\n    securityLicensePolicy = { deny, warn };\n  } else {\n    if (raw.securityLicensePolicy !== undefined) {\n      logWarn('Invalid config field securityLicensePolicy: expected object with deny/warn arrays, applying default');\n    }\n    securityLicensePolicy = defaults.securityLicensePolicy;\n  }\n\n  // \u2500\u2500 Patterns config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let enablePatterns: boolean;\n  if (typeof raw.enablePatterns === 'boolean') {\n    enablePatterns = raw.enablePatterns;\n  } else {\n    if (raw.enablePatterns !== undefined) {\n      logWarn('Invalid config field enablePatterns: expected boolean, applying default (false)');\n    }\n    enablePatterns = defaults.enablePatterns;\n  }\n\n  let patternLibraryPath: string | undefined;\n  if (raw.patternLibraryPath === undefined || raw.patternLibraryPath === null) {\n    patternLibraryPath = undefined;\n  } else if (typeof raw.patternLibraryPath === 'string') {\n    patternLibraryPath = raw.patternLibraryPath;\n  } else {\n    logWarn('Invalid config field patternLibraryPath: expected string or undefined, applying default (undefined)');\n    patternLibraryPath = defaults.patternLibraryPath;\n  }\n\n  const PATTERN_SEVERITY_LEVELS = new Set(['critical', 'high', 'medium', 'low']);\n  let patternSeverityThreshold: KiroGraphConfig['patternSeverityThreshold'];\n  if (typeof raw.patternSeverityThreshold === 'string' && PATTERN_SEVERITY_LEVELS.has(raw.patternSeverityThreshold)) {\n    patternSeverityThreshold = raw.patternSeverityThreshold as KiroGraphConfig['patternSeverityThreshold'];\n  } else {\n    if (raw.patternSeverityThreshold !== undefined) {\n      logWarn('Invalid config field patternSeverityThreshold: expected critical|high|medium|low, applying default (low)');\n    }\n    patternSeverityThreshold = defaults.patternSeverityThreshold;\n  }\n\n  // Dependency constraint: enableSecurity requires enableArchitecture\n  let finalEnableArchitecture = enableArchitecture;\n  if (enableSecurity && !enableArchitecture) {\n    logWarn('enableSecurity requires enableArchitecture \\u2014 auto-enabling architecture analysis');\n    finalEnableArchitecture = true;\n  }\n\n  // \u2500\u2500 Context budget config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let contextBudget: KiroGraphConfig['contextBudget'] | undefined;\n  if (raw.contextBudget && typeof raw.contextBudget === 'object' && !Array.isArray(raw.contextBudget)) {\n    const cb = raw.contextBudget as Record<string, unknown>;\n    contextBudget = {\n      maxTokensPerSession: typeof cb.maxTokensPerSession === 'number' && cb.maxTokensPerSession > 0\n        ? Math.round(cb.maxTokensPerSession) : 100_000,\n      warnAt: typeof cb.warnAt === 'number' && cb.warnAt > 0\n        ? Math.round(cb.warnAt) : 80_000,\n      throttleAt: typeof cb.throttleAt === 'number' && cb.throttleAt > 0\n        ? Math.round(cb.throttleAt) : 95_000,\n    };\n  }\n\n  // Validate glob patterns \u2014 exclude unsafe regex patterns\n  const include = _validatePatterns(raw.include, defaults.include);\n  const exclude = _validatePatterns(raw.exclude, defaults.exclude);\n\n  return {\n    version,\n    languages,\n    include,\n    exclude,\n    maxFileSize,\n    extractDocstrings,\n    trackCallSites,\n    enableEmbeddings,\n    embeddingModel,\n    embeddingDim,\n    useVecIndex,\n    semanticEngine,\n    typesenseDashboard,\n    qdrantDashboard,\n    minLogLevel,\n    frameworkHints,\n    fuzzyResolutionThreshold,\n    enableArchitecture: finalEnableArchitecture,\n    cavemanMode,\n    shellCompressionLevel,\n    syncWarningThreshold,\n    enableMemory,\n    memorySearchAlpha,\n    memoryKeepRaw,\n    memoryMaxObservations,\n    memorySessionTimeout,\n    memoryContextLimit,\n    memoryContextThreshold,\n    memoryExcludePatterns,\n    enableWatchmen: enableWatchmen && enableMemory,\n    watchmenThreshold,\n    watchmenSynthesisMode,\n    watchmenLocalModel,\n    enableDocs,\n    docsInclude,\n    docsExclude,\n    docsLinkCode,\n    docsContextLimit,\n    docsContextThreshold,\n    docsMaxFileSize,\n    docsSummarization,\n    enableData,\n    dataInclude,\n    dataExclude,\n    dataLinkCode,\n    dataContextLimit,\n    dataMaxFileSize,\n    dataMaxRows,\n    dataQueryLimit,\n    dataMaxResponseTokens,\n    enableSecurity,\n    securityDatabases,\n    securityAutoEnrich,\n    securityEnrichMaxAgeDays,\n    securityLicensePolicy,\n    enablePatterns,\n    patternLibraryPath,\n    patternSeverityThreshold,\n    ...(architectureLayers !== undefined ? { architectureLayers } : {}),\n    ...(contextBudget !== undefined ? { contextBudget } : {}),\n  };\n}\n\nfunction _validateArchitectureLayers(raw: unknown): Record<string, string[]> | undefined {\n  if (raw === undefined || raw === null) return undefined;\n  if (typeof raw !== 'object' || Array.isArray(raw)) return undefined;\n  const result: Record<string, string[]> = {};\n  for (const [key, val] of Object.entries(raw as Record<string, unknown>)) {\n    if (typeof key !== 'string') continue;\n    if (!Array.isArray(val)) continue;\n    const patterns = val.filter((p): p is string => typeof p === 'string' && isSafeRegex(p));\n    if (patterns.length > 0) result[key] = patterns;\n  }\n  return Object.keys(result).length > 0 ? result : undefined;\n}\n\nfunction _validatePatterns(raw: unknown, fallback: string[]): string[] {\n  if (!Array.isArray(raw)) return fallback;\n  const valid: string[] = [];\n  for (const p of raw) {\n    if (typeof p !== 'string') continue;\n    if (!isSafeRegex(p)) {\n      logWarn(`Unsafe regex pattern skipped: ${p}`);\n      continue;\n    }\n    valid.push(p);\n  }\n  return valid;\n}\n\n// \u2500\u2500 Migration helpers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Upgrades shallow exclude patterns (e.g. \"node_modules/**\") to recursive ones\n * (e.g. \"** /node_modules/**\") so nested directories are excluded at any depth.\n */\nconst SHALLOW_TO_RECURSIVE: Record<string, string> = {\n  'node_modules/**': '**/node_modules/**',\n  'dist/**': '**/dist/**',\n  'build/**': '**/build/**',\n  '.git/**': '**/.git/**',\n  '.kirograph/**': '**/.kirograph/**',\n};\n\nfunction migrateExcludePatterns(patterns: string[]): string[] {\n  return patterns.map(p => SHALLOW_TO_RECURSIVE[p] ?? p);\n}\n\n// \u2500\u2500 Load / Save \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport async function loadConfig(projectRoot: string): Promise<KiroGraphConfig> {\n  const dir = path.join(projectRoot, KIROGRAPH_DIR);\n  const cfgPath = path.join(dir, CONFIG_FILE);\n\n  if (!fs.existsSync(cfgPath)) {\n    // Create default config file\n    const defaults = createDefaultConfig(projectRoot);\n    await fs.promises.mkdir(dir, { recursive: true });\n    await _writeAtomic(cfgPath, defaults);\n    return defaults;\n  }\n\n  let raw: unknown;\n  try {\n    const text = await fs.promises.readFile(cfgPath, 'utf8');\n    raw = JSON.parse(text);\n  } catch (err) {\n    logError('Config parse error', { path: cfgPath, error: err instanceof Error ? err.message : String(err) });\n    return createDefaultConfig(projectRoot);\n  }\n\n  const config = validateConfig(raw);\n\n  // Migrate v1 \u2192 v2: upgrade shallow exclude patterns to recursive\n  if (config.version < 2) {\n    config.version = 2;\n    config.exclude = migrateExcludePatterns(config.exclude);\n    await fs.promises.mkdir(dir, { recursive: true });\n    await _writeAtomic(cfgPath, config);\n  }\n\n  return config;\n}\n\nexport async function saveConfig(projectRoot: string, config: KiroGraphConfig): Promise<void> {\n  const dir = path.join(projectRoot, KIROGRAPH_DIR);\n  const cfgPath = path.join(dir, CONFIG_FILE);\n  await fs.promises.mkdir(dir, { recursive: true });\n  await _writeAtomic(cfgPath, config);\n}\n\nasync function _writeAtomic(cfgPath: string, config: KiroGraphConfig): Promise<void> {\n  const tmp = cfgPath + '.tmp';\n  await fs.promises.writeFile(tmp, JSON.stringify(config, null, 2), 'utf8');\n  await fs.promises.rename(tmp, cfgPath);\n}\n\n// \u2500\u2500 Update helpers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport async function updateConfig(\n  projectRoot: string,\n  patch: Partial<KiroGraphConfig>\n): Promise<KiroGraphConfig> {\n  const current = await loadConfig(projectRoot);\n  const updated = validateConfig({ ...current, ...patch });\n  await saveConfig(projectRoot, updated);\n  return updated;\n}\n\nexport async function addIncludePatterns(projectRoot: string, patterns: string[]): Promise<void> {\n  const config = await loadConfig(projectRoot);\n  const existing = new Set(config.include);\n  const toAdd = patterns.filter(p => isSafeRegex(p) && !existing.has(p));\n  if (toAdd.length === 0) return;\n  await saveConfig(projectRoot, { ...config, include: [...config.include, ...toAdd] });\n}\n\nexport async function addExcludePatterns(projectRoot: string, patterns: string[]): Promise<void> {\n  const config = await loadConfig(projectRoot);\n  const existing = new Set(config.exclude);\n  const toAdd = patterns.filter(p => isSafeRegex(p) && !existing.has(p));\n  if (toAdd.length === 0) return;\n  await saveConfig(projectRoot, { ...config, exclude: [...config.exclude, ...toAdd] });\n}\n\n// \u2500\u2500 File inclusion check \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport function shouldIncludeFile(config: KiroGraphConfig, relPath: string): boolean {\n  // Check exclude patterns first\n  for (const pattern of config.exclude) {\n    if (picomatch(pattern)(relPath)) return false;\n  }\n  // If include patterns are specified, file must match at least one\n  if (config.include.length > 0) {\n    return config.include.some(pattern => picomatch(pattern)(relPath));\n  }\n  return true;\n}\n"],
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Kept for backwards compatibility. */\n  useVecIndex: boolean;\n  semanticEngine: 'cosine' | 'turboquant' | 'turbovec' | 'sqlite-vec' | 'orama' | 'pglite' | 'lancedb' | 'qdrant' | 'typesense';\n  /** Apply TurboQuant ANN index to memory observations and doc sections. Default: false. */\n  turboquantMemDocs: boolean;\n  /** TurboQuant bits per coordinate (1\u20138). Controls compression/quality tradeoff. Default: 3 (\u224825\u00D7). */\n  turboquantBits: number;\n  /** Apply TurboVec ANN index to memory observations and doc sections. Default: false. */\n  turbovecMemDocs: boolean;\n  /** TurboVec bits per coordinate (2, 3, or 4). Controls compression/quality tradeoff. Default: 4. */\n  turbovecBits: number;\n  typesenseDashboard: boolean;\n  qdrantDashboard: boolean;\n  minLogLevel: 'debug' | 'info' | 'warn' | 'error';\n  frameworkHints: string[];\n  fuzzyResolutionThreshold: number; // 0.0\u20131.0\n  /** Enable architecture analysis (package graph + layer detection). 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Default: 50MB. */\n  dataMaxFileSize: number;\n  /** Max rows to index per file. Default: 1,000,000. */\n  dataMaxRows: number;\n  /** Max rows returned per query. Default: 500. */\n  dataQueryLimit: number;\n  /** Max token budget per response. Default: 8000. */\n  dataMaxResponseTokens: number;\n  /** Enable security analysis (dependency scanning + vulnerability detection). Default: false. */\n  enableSecurity: boolean;\n  /** Vulnerability databases to query. Default: ['OSV']. */\n  securityDatabases: string[];\n  /** Enable AST-level structural pattern matching (SAST) during indexing. Default: false. */\n  enablePatterns: boolean;\n  /** Path to a directory of user-supplied YAML rule files. Merged with bundled library (user rules win on id conflict). Default: undefined. */\n  patternLibraryPath: string | undefined;\n  /** Minimum severity level for storing pattern matches during index-time analysis. Default: 'low'. */\n  patternSeverityThreshold: 'critical' | 'high' | 'medium' | 'low';\n  /** Auto-run vulnerability enrichment after manifest parsing. Default: true. */\n  securityAutoEnrich: boolean;\n  /** Max age in days for vulnerability data before showing a staleness warning. Default: 7. */\n  securityEnrichMaxAgeDays: number;\n  /**\n   * License policy for dependency compliance.\n   * deny: licenses to block (build fails / command exits non-zero).\n   * warn: licenses to flag as warnings.\n   * Patterns support wildcards: GPL-* matches GPL-2.0, GPL-3.0, etc.\n   * Default: { deny: [], warn: [] }.\n   */\n  securityLicensePolicy: {\n    deny: string[];\n    warn: string[];\n  };\n  /** Context budget governance settings. */\n  contextBudget?: {\n    maxTokensPerSession: number;\n    warnAt: number;\n    throttleAt: number;\n  };\n}\n\n// \u2500\u2500 Constants \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nconst KIROGRAPH_DIR = '.kirograph';\nconst CONFIG_FILE = 'config.json';\n\nconst KNOWN_FIELDS = new Set<string>([\n  'version', 'languages', 'include', 'exclude', 'maxFileSize',\n  'extractDocstrings', 'trackCallSites', 'enableEmbeddings', 'embeddingModel', 'embeddingDim',\n  'useVecIndex', 'semanticEngine', 'turboquantMemDocs', 'turboquantBits', 'turbovecMemDocs', 'turbovecBits', 'typesenseDashboard', 'qdrantDashboard',\n  'minLogLevel', 'frameworkHints', 'fuzzyResolutionThreshold',\n  'enableArchitecture', 'architectureLayers', 'cavemanMode', 'shellCompressionLevel', 'syncWarningThreshold',\n  'enableMemory', 'memorySearchAlpha', 'memoryKeepRaw', 'memoryMaxObservations',\n  'memorySessionTimeout', 'memoryContextLimit', 'memoryContextThreshold', 'memoryExcludePatterns',\n  'enableWatchmen', 'watchmenThreshold', 'watchmenSynthesisMode', 'watchmenLocalModel',\n  'enableDocs', 'docsInclude', 'docsExclude', 'docsLinkCode',\n  'docsContextLimit', 'docsContextThreshold', 'docsMaxFileSize', 'docsSummarization',\n  'enableData', 'dataInclude', 'dataExclude', 'dataLinkCode',\n  'dataContextLimit', 'dataMaxFileSize', 'dataMaxRows', 'dataQueryLimit', 'dataMaxResponseTokens',\n  'enableSecurity', 'securityDatabases', 'securityAutoEnrich', 'securityEnrichMaxAgeDays', 'securityLicensePolicy',\n  'enablePatterns', 'patternLibraryPath', 'patternSeverityThreshold',\n  'contextBudget',\n  // Legacy aliases (still accepted, mapped during validation)\n  'enableCompression', 'compressionLevel',\n]);\n\nconst LOG_LEVELS = new Set(['debug', 'info', 'warn', 'error']);\n\n// \u2500\u2500 ReDoS-safe regex check \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Returns false if the pattern is potentially dangerous (ReDoS risk) or too long.\n * Checks for catastrophic backtracking patterns like (a+)+ or (a|a)+.\n */\nexport function isSafeRegex(pattern: string): boolean {\n  if (pattern.length > 100) return false;\n  // Detect nested quantifiers: (x+)+ or (x*)+ or (x+)* etc.\n  if (/\\([^)]*[+*][^)]*\\)[+*?]/.test(pattern)) return false;\n  // Detect alternation with overlap: (a|a)+ style\n  if (/\\([^)]*\\|[^)]*\\)[+*]/.test(pattern)) return false;\n  return true;\n}\n\n// \u2500\u2500 Default config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport function createDefaultConfig(_projectRoot?: string): KiroGraphConfig {\n  return {\n    version: 2,\n    languages: [],\n    include: [],\n    exclude: ['**/node_modules/**', '**/dist/**', '**/build/**', '**/.git/**', '*.min.js', '**/.kirograph/**'],\n    maxFileSize: 1_048_576,\n    extractDocstrings: true,\n    trackCallSites: true,\n    enableEmbeddings: false,\n    embeddingModel: 'nomic-ai/nomic-embed-text-v1.5',\n    embeddingDim: 768,\n    useVecIndex: false,\n    semanticEngine: 'cosine',\n    turboquantMemDocs: false,\n    turboquantBits: 3,\n    turbovecMemDocs: false,\n    turbovecBits: 4,\n    typesenseDashboard: false,\n    qdrantDashboard: false,\n    minLogLevel: 'warn',\n    frameworkHints: [],\n    fuzzyResolutionThreshold: 0.5,\n    enableArchitecture: false,\n    cavemanMode: 'off',\n    shellCompressionLevel: 'normal',\n    syncWarningThreshold: 10,\n    enableMemory: false,\n    memorySearchAlpha: 0.5,\n    memoryKeepRaw: false,\n    memoryMaxObservations: 10000,\n    memorySessionTimeout: 7200,\n    memoryContextLimit: 3,\n    memoryContextThreshold: 0.3,\n    memoryExcludePatterns: [],\n    enableWatchmen: false,\n    watchmenThreshold: 5,\n    watchmenSynthesisMode: 'local',\n    watchmenLocalModel: 'onnx-community/gemma-4-E4B-it-ONNX',\n    enableDocs: false,\n    docsInclude: ['**/*.md', '**/*.mdx', '**/*.rst', '**/*.adoc', '**/*.asciidoc', '**/*.rdoc', '**/*.org', '**/*.cheatmd', 'docs/**/*.txt', 'docs/**/*.html'],\n    docsExclude: ['node_modules/**', '**/CHANGELOG*', '**/LICENSE*', '**/CHANGES*', 'dist/**', 'build/**', 'coverage/**', '.git/**', '**/generated/**', '**/auto-generated/**', '**/vendor/**', '_build/**'],\n    docsLinkCode: true,\n    docsContextLimit: 0,\n    docsContextThreshold: 0.3,\n    docsMaxFileSize: 1_048_576,\n    docsSummarization: 'first-sentence',\n    enableData: false,\n    dataInclude: ['**/*.csv', '**/*.tsv', '**/*.jsonl', '**/*.ndjson', '**/*.xlsx', '**/*.xls', '**/*.parquet', 'data/**/*.json', '**/*.pdf'],\n    dataExclude: ['node_modules/**', 'dist/**', 'build/**', '.git/**', '**/package-lock.json', '**/yarn.lock', '**/pnpm-lock.yaml', '**/tsconfig.json', '**/jsconfig.json', 'coverage/**', '**/generated/**'],\n    dataLinkCode: true,\n    dataContextLimit: 0,\n    dataMaxFileSize: 52_428_800,\n    dataMaxRows: 1_000_000,\n    dataQueryLimit: 500,\n    dataMaxResponseTokens: 8000,\n    enableSecurity: false,\n    securityDatabases: ['OSV'],\n    securityAutoEnrich: true,\n    securityEnrichMaxAgeDays: 7,\n    securityLicensePolicy: { deny: [], warn: [] },\n    enablePatterns: false,\n    patternLibraryPath: undefined,\n    patternSeverityThreshold: 'low',\n  };\n}\n\n// \u2500\u2500 Validation \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport function validateConfig(config: unknown): KiroGraphConfig {\n  const defaults = createDefaultConfig();\n\n  if (typeof config !== 'object' || config === null) {\n    return defaults;\n  }\n\n  const raw = config as Record<string, unknown>;\n\n  // Warn about unknown fields\n  for (const key of Object.keys(raw)) {\n    if (!KNOWN_FIELDS.has(key)) {\n      logWarn(`Unknown config field: ${key}`);\n    }\n  }\n\n  // Validate and coerce each field\n  const version = typeof raw.version === 'number' ? raw.version : defaults.version;\n  const languages = Array.isArray(raw.languages) && raw.languages.every(l => typeof l === 'string')\n    ? (raw.languages as string[])\n    : defaults.languages;\n  const maxFileSize = typeof raw.maxFileSize === 'number' && raw.maxFileSize > 0\n    ? raw.maxFileSize\n    : defaults.maxFileSize;\n  const extractDocstrings = typeof raw.extractDocstrings === 'boolean'\n    ? raw.extractDocstrings\n    : defaults.extractDocstrings;\n  const trackCallSites = typeof raw.trackCallSites === 'boolean'\n    ? raw.trackCallSites\n    : defaults.trackCallSites;\n  const enableEmbeddings = typeof raw.enableEmbeddings === 'boolean'\n    ? raw.enableEmbeddings\n    : defaults.enableEmbeddings;\n  const embeddingModel = typeof raw.embeddingModel === 'string' && raw.embeddingModel.length > 0\n    ? raw.embeddingModel\n    : defaults.embeddingModel;\n  const embeddingDim = typeof raw.embeddingDim === 'number' && raw.embeddingDim > 0\n    ? raw.embeddingDim\n    : defaults.embeddingDim;\n  const useVecIndex = typeof raw.useVecIndex === 'boolean'\n    ? raw.useVecIndex\n    : defaults.useVecIndex;\n  const SEMANTIC_ENGINES = new Set(['cosine', 'turboquant', 'turbovec', 'sqlite-vec', 'orama', 'pglite', 'lancedb', 'qdrant', 'typesense']);\n  // useVecIndex is a legacy alias: if set and no explicit semanticEngine, map it\n  const semanticEngine = typeof raw.semanticEngine === 'string' && SEMANTIC_ENGINES.has(raw.semanticEngine)\n    ? (raw.semanticEngine as KiroGraphConfig['semanticEngine'])\n    : useVecIndex ? 'sqlite-vec' : defaults.semanticEngine;\n  const turboquantMemDocs = typeof raw.turboquantMemDocs === 'boolean'\n    ? raw.turboquantMemDocs\n    : defaults.turboquantMemDocs;\n  const turboquantBits = typeof raw.turboquantBits === 'number'\n    && raw.turboquantBits >= 1 && raw.turboquantBits <= 8\n    ? Math.round(raw.turboquantBits)\n    : defaults.turboquantBits;\n  const turbovecMemDocs = typeof raw.turbovecMemDocs === 'boolean'\n    ? raw.turbovecMemDocs\n    : defaults.turbovecMemDocs;\n  const TURBOVEC_BIT_WIDTHS = new Set([2, 3, 4]);\n  const turbovecBits = typeof raw.turbovecBits === 'number' && TURBOVEC_BIT_WIDTHS.has(Math.round(raw.turbovecBits))\n    ? Math.round(raw.turbovecBits)\n    : defaults.turbovecBits;\n  const typesenseDashboard = typeof raw.typesenseDashboard === 'boolean'\n    ? raw.typesenseDashboard\n    : defaults.typesenseDashboard;\n  const qdrantDashboard = typeof raw.qdrantDashboard === 'boolean'\n    ? raw.qdrantDashboard\n    : defaults.qdrantDashboard;\n  const minLogLevel = typeof raw.minLogLevel === 'string' && LOG_LEVELS.has(raw.minLogLevel)\n    ? (raw.minLogLevel as KiroGraphConfig['minLogLevel'])\n    : defaults.minLogLevel;\n  const frameworkHints = Array.isArray(raw.frameworkHints) && raw.frameworkHints.every(h => typeof h === 'string')\n    ? (raw.frameworkHints as string[])\n    : defaults.frameworkHints;\n  const fuzzyResolutionThreshold = typeof raw.fuzzyResolutionThreshold === 'number'\n    && raw.fuzzyResolutionThreshold >= 0\n    && raw.fuzzyResolutionThreshold <= 1\n    ? raw.fuzzyResolutionThreshold\n    : defaults.fuzzyResolutionThreshold;\n  const enableArchitecture = typeof raw.enableArchitecture === 'boolean'\n    ? raw.enableArchitecture\n    : defaults.enableArchitecture;\n  const architectureLayers = _validateArchitectureLayers(raw.architectureLayers);\n  const CAVEMAN_MODES = new Set(['off', 'lite', 'full', 'ultra']);\n  const cavemanMode = typeof raw.cavemanMode === 'string' && CAVEMAN_MODES.has(raw.cavemanMode)\n    ? (raw.cavemanMode as KiroGraphConfig['cavemanMode'])\n    : defaults.cavemanMode;\n  const COMPRESSION_LEVELS = new Set(['off', 'normal', 'aggressive', 'ultra']);\n  // Support legacy field names: enableCompression (boolean) and compressionLevel (string)\n  let shellCompressionLevel: KiroGraphConfig['shellCompressionLevel'];\n  if (typeof raw.shellCompressionLevel === 'string' && COMPRESSION_LEVELS.has(raw.shellCompressionLevel)) {\n    shellCompressionLevel = raw.shellCompressionLevel as KiroGraphConfig['shellCompressionLevel'];\n  } else if (typeof raw.compressionLevel === 'string' && COMPRESSION_LEVELS.has(raw.compressionLevel)) {\n    shellCompressionLevel = raw.compressionLevel as KiroGraphConfig['shellCompressionLevel'];\n  } else if (typeof raw.enableCompression === 'boolean') {\n    shellCompressionLevel = raw.enableCompression ? 'normal' : 'off';\n  } else {\n    shellCompressionLevel = defaults.shellCompressionLevel;\n  }\n  const syncWarningThreshold = typeof raw.syncWarningThreshold === 'number' && raw.syncWarningThreshold >= 0\n    ? Math.round(raw.syncWarningThreshold)\n    : defaults.syncWarningThreshold;\n\n  // \u2500\u2500 Memory config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const enableMemory = typeof raw.enableMemory === 'boolean'\n    ? raw.enableMemory\n    : defaults.enableMemory;\n  const memorySearchAlpha = typeof raw.memorySearchAlpha === 'number'\n    && raw.memorySearchAlpha >= 0 && raw.memorySearchAlpha <= 1\n    ? raw.memorySearchAlpha\n    : defaults.memorySearchAlpha;\n  const memoryKeepRaw = typeof raw.memoryKeepRaw === 'boolean'\n    ? raw.memoryKeepRaw\n    : defaults.memoryKeepRaw;\n  const memoryMaxObservations = typeof raw.memoryMaxObservations === 'number' && raw.memoryMaxObservations >= 0\n    ? Math.round(raw.memoryMaxObservations)\n    : defaults.memoryMaxObservations;\n  const memorySessionTimeout = typeof raw.memorySessionTimeout === 'number' && raw.memorySessionTimeout > 0\n    ? Math.round(raw.memorySessionTimeout)\n    : defaults.memorySessionTimeout;\n  const memoryContextLimit = typeof raw.memoryContextLimit === 'number' && raw.memoryContextLimit >= 0\n    ? Math.round(raw.memoryContextLimit)\n    : defaults.memoryContextLimit;\n  const memoryContextThreshold = typeof raw.memoryContextThreshold === 'number'\n    && raw.memoryContextThreshold >= 0 && raw.memoryContextThreshold <= 1\n    ? raw.memoryContextThreshold\n    : defaults.memoryContextThreshold;\n  const memoryExcludePatterns = Array.isArray(raw.memoryExcludePatterns)\n    && raw.memoryExcludePatterns.every((p: unknown) => typeof p === 'string')\n    ? (raw.memoryExcludePatterns as string[])\n    : defaults.memoryExcludePatterns;\n\n  // \u2500\u2500 Watchmen config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const enableWatchmen = typeof raw.enableWatchmen === 'boolean'\n    ? raw.enableWatchmen\n    : defaults.enableWatchmen;\n  const watchmenThreshold = typeof raw.watchmenThreshold === 'number' && raw.watchmenThreshold > 0\n    ? Math.round(raw.watchmenThreshold)\n    : defaults.watchmenThreshold;\n  const WATCHMEN_SYNTHESIS_MODES = new Set(['local', 'agent']);\n  const watchmenSynthesisMode = typeof raw.watchmenSynthesisMode === 'string' && WATCHMEN_SYNTHESIS_MODES.has(raw.watchmenSynthesisMode)\n    ? (raw.watchmenSynthesisMode as KiroGraphConfig['watchmenSynthesisMode'])\n    : defaults.watchmenSynthesisMode;\n  const watchmenLocalModel = typeof raw.watchmenLocalModel === 'string' && raw.watchmenLocalModel.length > 0\n    ? raw.watchmenLocalModel\n    : defaults.watchmenLocalModel;\n\n  // \u2500\u2500 Docs config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const enableDocs = typeof raw.enableDocs === 'boolean'\n    ? raw.enableDocs\n    : defaults.enableDocs;\n  const docsInclude = Array.isArray(raw.docsInclude)\n    && raw.docsInclude.every((p: unknown) => typeof p === 'string')\n    ? (raw.docsInclude as string[])\n    : defaults.docsInclude;\n  const docsExclude = Array.isArray(raw.docsExclude)\n    && raw.docsExclude.every((p: unknown) => typeof p === 'string')\n    ? (raw.docsExclude as string[])\n    : defaults.docsExclude;\n  const docsLinkCode = typeof raw.docsLinkCode === 'boolean'\n    ? raw.docsLinkCode\n    : defaults.docsLinkCode;\n  const docsContextLimit = typeof raw.docsContextLimit === 'number' && raw.docsContextLimit >= 0\n    ? Math.round(raw.docsContextLimit)\n    : defaults.docsContextLimit;\n  const docsContextThreshold = typeof raw.docsContextThreshold === 'number'\n    && raw.docsContextThreshold >= 0 && raw.docsContextThreshold <= 1\n    ? raw.docsContextThreshold\n    : defaults.docsContextThreshold;\n  const docsMaxFileSize = typeof raw.docsMaxFileSize === 'number' && raw.docsMaxFileSize > 0\n    ? raw.docsMaxFileSize\n    : defaults.docsMaxFileSize;\n  const DOCS_SUMMARIZATION_MODES = new Set(['embedding', 'first-sentence', 'off']);\n  const docsSummarization = typeof raw.docsSummarization === 'string' && DOCS_SUMMARIZATION_MODES.has(raw.docsSummarization)\n    ? (raw.docsSummarization as KiroGraphConfig['docsSummarization'])\n    : defaults.docsSummarization;\n\n  // \u2500\u2500 Data config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const enableData = typeof raw.enableData === 'boolean' ? raw.enableData : defaults.enableData;\n  const dataInclude = Array.isArray(raw.dataInclude) && raw.dataInclude.every((p: unknown) => typeof p === 'string')\n    ? (raw.dataInclude as string[]) : defaults.dataInclude;\n  const dataExclude = Array.isArray(raw.dataExclude) && raw.dataExclude.every((p: unknown) => typeof p === 'string')\n    ? (raw.dataExclude as string[]) : defaults.dataExclude;\n  const dataLinkCode = typeof raw.dataLinkCode === 'boolean' ? raw.dataLinkCode : defaults.dataLinkCode;\n  const dataContextLimit = typeof raw.dataContextLimit === 'number' && raw.dataContextLimit >= 0\n    ? Math.round(raw.dataContextLimit) : defaults.dataContextLimit;\n  const dataMaxFileSize = typeof raw.dataMaxFileSize === 'number' && raw.dataMaxFileSize > 0\n    ? raw.dataMaxFileSize : defaults.dataMaxFileSize;\n  const dataMaxRows = typeof raw.dataMaxRows === 'number' && raw.dataMaxRows > 0\n    ? Math.round(raw.dataMaxRows) : defaults.dataMaxRows;\n  const dataQueryLimit = typeof raw.dataQueryLimit === 'number' && raw.dataQueryLimit > 0\n    ? Math.min(Math.round(raw.dataQueryLimit), 500) : defaults.dataQueryLimit;\n  const dataMaxResponseTokens = typeof raw.dataMaxResponseTokens === 'number' && raw.dataMaxResponseTokens > 0\n    ? Math.round(raw.dataMaxResponseTokens) : defaults.dataMaxResponseTokens;\n\n  // \u2500\u2500 Security config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let enableSecurity: boolean;\n  if (typeof raw.enableSecurity === 'boolean') {\n    enableSecurity = raw.enableSecurity;\n  } else {\n    if (raw.enableSecurity !== undefined) {\n      logWarn('Invalid config field enableSecurity: expected boolean, applying default (false)');\n    }\n    enableSecurity = defaults.enableSecurity;\n  }\n\n  let securityAutoEnrich: boolean;\n  if (typeof raw.securityAutoEnrich === 'boolean') {\n    securityAutoEnrich = raw.securityAutoEnrich;\n  } else {\n    if (raw.securityAutoEnrich !== undefined) {\n      logWarn('Invalid config field securityAutoEnrich: expected boolean, applying default (true)');\n    }\n    securityAutoEnrich = defaults.securityAutoEnrich;\n  }\n\n  let securityEnrichMaxAgeDays: number;\n  if (typeof raw.securityEnrichMaxAgeDays === 'number' && raw.securityEnrichMaxAgeDays > 0) {\n    securityEnrichMaxAgeDays = raw.securityEnrichMaxAgeDays;\n  } else {\n    if (raw.securityEnrichMaxAgeDays !== undefined) {\n      logWarn('Invalid config field securityEnrichMaxAgeDays: expected positive number, applying default (7)');\n    }\n    securityEnrichMaxAgeDays = defaults.securityEnrichMaxAgeDays;\n  }\n\n  const SUPPORTED_SECURITY_DATABASES = new Set(['OSV']);\n  let securityDatabases: string[];\n  if (Array.isArray(raw.securityDatabases) && raw.securityDatabases.every((d: unknown) => typeof d === 'string')) {\n    const valid = (raw.securityDatabases as string[]).filter(d => {\n      if (!SUPPORTED_SECURITY_DATABASES.has(d)) {\n        logWarn(`Unsupported security database \"${d}\" in securityDatabases, ignoring`);\n        return false;\n      }\n      return true;\n    });\n    securityDatabases = valid.length > 0 ? valid : defaults.securityDatabases;\n  } else {\n    if (raw.securityDatabases !== undefined) {\n      logWarn('Invalid config field securityDatabases: expected array of strings, applying default ([\"OSV\"])');\n    }\n    securityDatabases = defaults.securityDatabases;\n  }\n\n  let securityLicensePolicy: KiroGraphConfig['securityLicensePolicy'];\n  if (raw.securityLicensePolicy && typeof raw.securityLicensePolicy === 'object' && !Array.isArray(raw.securityLicensePolicy)) {\n    const rawPolicy = raw.securityLicensePolicy as Record<string, unknown>;\n    const deny = Array.isArray(rawPolicy.deny) && rawPolicy.deny.every((p: unknown) => typeof p === 'string')\n      ? (rawPolicy.deny as string[])\n      : defaults.securityLicensePolicy.deny;\n    const warn = Array.isArray(rawPolicy.warn) && rawPolicy.warn.every((p: unknown) => typeof p === 'string')\n      ? (rawPolicy.warn as string[])\n      : defaults.securityLicensePolicy.warn;\n    securityLicensePolicy = { deny, warn };\n  } else {\n    if (raw.securityLicensePolicy !== undefined) {\n      logWarn('Invalid config field securityLicensePolicy: expected object with deny/warn arrays, applying default');\n    }\n    securityLicensePolicy = defaults.securityLicensePolicy;\n  }\n\n  // \u2500\u2500 Patterns config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let enablePatterns: boolean;\n  if (typeof raw.enablePatterns === 'boolean') {\n    enablePatterns = raw.enablePatterns;\n  } else {\n    if (raw.enablePatterns !== undefined) {\n      logWarn('Invalid config field enablePatterns: expected boolean, applying default (false)');\n    }\n    enablePatterns = defaults.enablePatterns;\n  }\n\n  let patternLibraryPath: string | undefined;\n  if (raw.patternLibraryPath === undefined || raw.patternLibraryPath === null) {\n    patternLibraryPath = undefined;\n  } else if (typeof raw.patternLibraryPath === 'string') {\n    patternLibraryPath = raw.patternLibraryPath;\n  } else {\n    logWarn('Invalid config field patternLibraryPath: expected string or undefined, applying default (undefined)');\n    patternLibraryPath = defaults.patternLibraryPath;\n  }\n\n  const PATTERN_SEVERITY_LEVELS = new Set(['critical', 'high', 'medium', 'low']);\n  let patternSeverityThreshold: KiroGraphConfig['patternSeverityThreshold'];\n  if (typeof raw.patternSeverityThreshold === 'string' && PATTERN_SEVERITY_LEVELS.has(raw.patternSeverityThreshold)) {\n    patternSeverityThreshold = raw.patternSeverityThreshold as KiroGraphConfig['patternSeverityThreshold'];\n  } else {\n    if (raw.patternSeverityThreshold !== undefined) {\n      logWarn('Invalid config field patternSeverityThreshold: expected critical|high|medium|low, applying default (low)');\n    }\n    patternSeverityThreshold = defaults.patternSeverityThreshold;\n  }\n\n  // Dependency constraint: enableSecurity requires enableArchitecture\n  let finalEnableArchitecture = enableArchitecture;\n  if (enableSecurity && !enableArchitecture) {\n    logWarn('enableSecurity requires enableArchitecture \\u2014 auto-enabling architecture analysis');\n    finalEnableArchitecture = true;\n  }\n\n  // \u2500\u2500 Context budget config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let contextBudget: KiroGraphConfig['contextBudget'] | undefined;\n  if (raw.contextBudget && typeof raw.contextBudget === 'object' && !Array.isArray(raw.contextBudget)) {\n    const cb = raw.contextBudget as Record<string, unknown>;\n    contextBudget = {\n      maxTokensPerSession: typeof cb.maxTokensPerSession === 'number' && cb.maxTokensPerSession > 0\n        ? Math.round(cb.maxTokensPerSession) : 100_000,\n      warnAt: typeof cb.warnAt === 'number' && cb.warnAt > 0\n        ? Math.round(cb.warnAt) : 80_000,\n      throttleAt: typeof cb.throttleAt === 'number' && cb.throttleAt > 0\n        ? Math.round(cb.throttleAt) : 95_000,\n    };\n  }\n\n  // Validate glob patterns \u2014 exclude unsafe regex patterns\n  const include = _validatePatterns(raw.include, defaults.include);\n  const exclude = _validatePatterns(raw.exclude, defaults.exclude);\n\n  return {\n    version,\n    languages,\n    include,\n    exclude,\n    maxFileSize,\n    extractDocstrings,\n    trackCallSites,\n    enableEmbeddings,\n    embeddingModel,\n    embeddingDim,\n    useVecIndex,\n    semanticEngine,\n    turboquantMemDocs,\n    turboquantBits,\n    turbovecMemDocs,\n    turbovecBits,\n    typesenseDashboard,\n    qdrantDashboard,\n    minLogLevel,\n    frameworkHints,\n    fuzzyResolutionThreshold,\n    enableArchitecture: finalEnableArchitecture,\n    cavemanMode,\n    shellCompressionLevel,\n    syncWarningThreshold,\n    enableMemory,\n    memorySearchAlpha,\n    memoryKeepRaw,\n    memoryMaxObservations,\n    memorySessionTimeout,\n    memoryContextLimit,\n    memoryContextThreshold,\n    memoryExcludePatterns,\n    enableWatchmen: enableWatchmen && enableMemory,\n    watchmenThreshold,\n    watchmenSynthesisMode,\n    watchmenLocalModel,\n    enableDocs,\n    docsInclude,\n    docsExclude,\n    docsLinkCode,\n    docsContextLimit,\n    docsContextThreshold,\n    docsMaxFileSize,\n    docsSummarization,\n    enableData,\n    dataInclude,\n    dataExclude,\n    dataLinkCode,\n    dataContextLimit,\n    dataMaxFileSize,\n    dataMaxRows,\n    dataQueryLimit,\n    dataMaxResponseTokens,\n    enableSecurity,\n    securityDatabases,\n    securityAutoEnrich,\n    securityEnrichMaxAgeDays,\n    securityLicensePolicy,\n    enablePatterns,\n    patternLibraryPath,\n    patternSeverityThreshold,\n    ...(architectureLayers !== undefined ? { architectureLayers } : {}),\n    ...(contextBudget !== undefined ? { contextBudget } : {}),\n  };\n}\n\nfunction _validateArchitectureLayers(raw: unknown): Record<string, string[]> | undefined {\n  if (raw === undefined || raw === null) return undefined;\n  if (typeof raw !== 'object' || Array.isArray(raw)) return undefined;\n  const result: Record<string, string[]> = {};\n  for (const [key, val] of Object.entries(raw as Record<string, unknown>)) {\n    if (typeof key !== 'string') continue;\n    if (!Array.isArray(val)) continue;\n    const patterns = val.filter((p): p is string => typeof p === 'string' && isSafeRegex(p));\n    if (patterns.length > 0) result[key] = patterns;\n  }\n  return Object.keys(result).length > 0 ? result : undefined;\n}\n\nfunction _validatePatterns(raw: unknown, fallback: string[]): string[] {\n  if (!Array.isArray(raw)) return fallback;\n  const valid: string[] = [];\n  for (const p of raw) {\n    if (typeof p !== 'string') continue;\n    if (!isSafeRegex(p)) {\n      logWarn(`Unsafe regex pattern skipped: ${p}`);\n      continue;\n    }\n    valid.push(p);\n  }\n  return valid;\n}\n\n// \u2500\u2500 Migration helpers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Upgrades shallow exclude patterns (e.g. \"node_modules/**\") to recursive ones\n * (e.g. \"** /node_modules/**\") so nested directories are excluded at any depth.\n */\nconst SHALLOW_TO_RECURSIVE: Record<string, string> = {\n  'node_modules/**': '**/node_modules/**',\n  'dist/**': '**/dist/**',\n  'build/**': '**/build/**',\n  '.git/**': '**/.git/**',\n  '.kirograph/**': '**/.kirograph/**',\n};\n\nfunction migrateExcludePatterns(patterns: string[]): string[] {\n  return patterns.map(p => SHALLOW_TO_RECURSIVE[p] ?? p);\n}\n\n// \u2500\u2500 Load / Save \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport async function loadConfig(projectRoot: string): Promise<KiroGraphConfig> {\n  const dir = path.join(projectRoot, KIROGRAPH_DIR);\n  const cfgPath = path.join(dir, CONFIG_FILE);\n\n  if (!fs.existsSync(cfgPath)) {\n    // Create default config file\n    const defaults = createDefaultConfig(projectRoot);\n    await fs.promises.mkdir(dir, { recursive: true });\n    await _writeAtomic(cfgPath, defaults);\n    return defaults;\n  }\n\n  let raw: unknown;\n  try {\n    const text = await fs.promises.readFile(cfgPath, 'utf8');\n    raw = JSON.parse(text);\n  } catch (err) {\n    logError('Config parse error', { path: cfgPath, error: err instanceof Error ? err.message : String(err) });\n    return createDefaultConfig(projectRoot);\n  }\n\n  const config = validateConfig(raw);\n\n  // Migrate v1 \u2192 v2: upgrade shallow exclude patterns to recursive\n  if (config.version < 2) {\n    config.version = 2;\n    config.exclude = migrateExcludePatterns(config.exclude);\n    await fs.promises.mkdir(dir, { recursive: true });\n    await _writeAtomic(cfgPath, config);\n  }\n\n  return config;\n}\n\nexport async function saveConfig(projectRoot: string, config: KiroGraphConfig): Promise<void> {\n  const dir = path.join(projectRoot, KIROGRAPH_DIR);\n  const cfgPath = path.join(dir, CONFIG_FILE);\n  await fs.promises.mkdir(dir, { recursive: true });\n  await _writeAtomic(cfgPath, config);\n}\n\nasync function _writeAtomic(cfgPath: string, config: KiroGraphConfig): Promise<void> {\n  const tmp = cfgPath + '.tmp';\n  await fs.promises.writeFile(tmp, JSON.stringify(config, null, 2), 'utf8');\n  await fs.promises.rename(tmp, cfgPath);\n}\n\n// \u2500\u2500 Update helpers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport async function updateConfig(\n  projectRoot: string,\n  patch: Partial<KiroGraphConfig>\n): Promise<KiroGraphConfig> {\n  const current = await loadConfig(projectRoot);\n  const updated = validateConfig({ ...current, ...patch });\n  await saveConfig(projectRoot, updated);\n  return updated;\n}\n\nexport async function addIncludePatterns(projectRoot: string, patterns: string[]): Promise<void> {\n  const config = await loadConfig(projectRoot);\n  const existing = new Set(config.include);\n  const toAdd = patterns.filter(p => isSafeRegex(p) && !existing.has(p));\n  if (toAdd.length === 0) return;\n  await saveConfig(projectRoot, { ...config, include: [...config.include, ...toAdd] });\n}\n\nexport async function addExcludePatterns(projectRoot: string, patterns: string[]): Promise<void> {\n  const config = await loadConfig(projectRoot);\n  const existing = new Set(config.exclude);\n  const toAdd = patterns.filter(p => isSafeRegex(p) && !existing.has(p));\n  if (toAdd.length === 0) return;\n  await saveConfig(projectRoot, { ...config, exclude: [...config.exclude, ...toAdd] });\n}\n\n// \u2500\u2500 File inclusion check \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport function shouldIncludeFile(config: KiroGraphConfig, relPath: string): boolean {\n  // Check exclude patterns first\n  for (const pattern of config.exclude) {\n    if (picomatch(pattern)(relPath)) return false;\n  }\n  // If include patterns are specified, file must match at least one\n  if (config.include.length > 0) {\n    return config.include.some(pattern => picomatch(pattern)(relPath));\n  }\n  return true;\n}\n"],
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   "names": ["picomatch"]
 }

package/dist/core/pipeline.js

@@ -305,7 +305,9 @@ class IndexPipeline {
         await this.vectors.deleteEmbeddings(oldNodes.map((n) => n.id));
         this.db.deleteFile(rel);
         this.db.deleteUnresolvedRefsByFile(rel);
-        this.db.getRawDb().run("DELETE FROM pattern_matches WHERE file_path = ?", [rel]);
+        if (this.config.enablePatterns) {
+          this.db.getRawDb().run("DELETE FROM pattern_matches WHERE file_path = ?", [rel]);
+        }
         result.removed.push(rel);
       };
       const allIndexed = this.db.getAllFiles();

package/dist/core/pipeline.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/pipeline.ts"],
-  "sourcesContent": ["/**\n * IndexPipeline \u2014 full-index and incremental-sync pipelines.\n *\n * Owns the two heavy workflows:\n *   - indexAll(): scan all files, extract, store, resolve, detect frameworks,\n *                 generate embeddings, analyze architecture.\n *   - sync():     detect changed files via git (or full scan fallback),\n *                 re-extract only what changed, then run the same tail pipeline.\n *\n * Everything that touches the filesystem or sub-systems is injected via the\n * constructor, keeping this class testable and free of global state.\n */\n\nimport * as path from 'path';\nimport * as fs from 'fs';\nimport { GraphDatabase } from '../db/database';\nimport { scanDirectory, hashContent, getChangedFiles, shouldIncludeFile } from '../sync/index';\nimport { extractFile } from '../extraction/extractor';\nimport { clearParserCache, initGrammars, hasWasmGrammar } from '../extraction/grammars';\nimport { detectFrameworks } from '../frameworks/index';\nimport { ReferenceResolver } from '../resolution/index';\nimport { VectorManager } from '../vectors/index';\nimport { ArchitectureAnalyzer } from '../architecture/index';\nimport type { KiroGraphConfig } from '../config';\nimport type { IndexResult, IndexProgress, SyncResult } from '../types';\nimport { LockManager } from './lock-manager';\nimport { Mutex } from '../utils';\n\nconst FILE_IO_BATCH_SIZE = 10;\n\nexport class IndexPipeline {\n  private readonly mutex = new Mutex();\n\n  constructor(\n    private readonly db: GraphDatabase,\n    private readonly vectors: VectorManager,\n    private readonly resolver: ReferenceResolver,\n    private readonly arch: ArchitectureAnalyzer,\n    private readonly lock: LockManager,\n    private readonly config: KiroGraphConfig,\n    private readonly projectRoot: string,\n  ) {}\n\n  async indexAll(opts?: {\n    onProgress?: (p: IndexProgress) => void;\n    force?: boolean;\n    signal?: AbortSignal;\n  }): Promise<IndexResult> {\n    const release = await this.mutex.acquire();\n    this.lock.acquire();\n    const start = Date.now();\n    const errors: string[] = [];\n    let filesIndexed = 0;\n    let nodesCreated = 0;\n    let edgesCreated = 0;\n\n    // Track languages whose WASM parser is currently poisoned (ABORT=true on the module).\n    // Once a language's parser aborts, every subsequent parse call for that language\n    // fails instantly. We skip those files until clearParserCache + initGrammars succeeds.\n    const poisonedLanguages = new Set<string>();\n\n    try {\n      const files = await scanDirectory(this.projectRoot, this.config, opts?.signal);\n      opts?.onProgress?.({ phase: 'scanning', current: files.length, total: files.length });\n\n      // Batch-read files in parallel\n      const contentMap = new Map<string, Buffer>();\n      for (let b = 0; b < files.length; b += FILE_IO_BATCH_SIZE) {\n        const batch = files.slice(b, b + FILE_IO_BATCH_SIZE);\n        const results = await Promise.all(batch.map(f => fs.promises.readFile(f).catch(() => null)));\n        for (let i = 0; i < batch.length; i++) {\n          if (results[i]) contentMap.set(batch[i], results[i]!);\n        }\n      }\n\n      for (let i = 0; i < files.length; i++) {\n        const file = files[i];\n        opts?.onProgress?.({ phase: 'parsing', current: i + 1, total: files.length, currentFile: file });\n\n        try {\n          const content = contentMap.get(file);\n          if (!content) continue;\n          if (content.length > this.config.maxFileSize) continue;\n\n          const relPath = path.relative(this.projectRoot, file).replace(/\\\\/g, '/');\n\n          if (!opts?.force) {\n            const existing = this.db.getFile(relPath);\n            if (existing && hashContent(content) === existing.contentHash) continue;\n          }\n\n          // Skip files whose language parser is currently poisoned\n          const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n          const lang = detectLanguage(file);\n          if (poisonedLanguages.has(lang)) continue;\n\n          const extracted = await extractFile(file, this.projectRoot, content);\n          if (!extracted) continue;\n\n          const oldNodes = this.db.getNodesByFile(extracted.filePath);\n          if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n          this.db.transaction(() => {\n            this.db.deleteNodesByFile(extracted.filePath);\n            this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n            this.db.upsertFile({\n              path: extracted.filePath,\n              contentHash: extracted.contentHash,\n              language: extracted.language,\n              fileSize: extracted.fileSize,\n              symbolCount: extracted.nodes.length,\n              indexedAt: Date.now(),\n            });\n            for (const node of extracted.nodes) { this.db.upsertNode(node); nodesCreated++; }\n            for (const edge of extracted.edges) { this.db.insertEdge(edge); edgesCreated++; }\n            for (const ref of extracted.unresolvedRefs) {\n              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n            }\n          });\n\n          filesIndexed++;\n        } catch (err) {\n          const msg = err instanceof Error ? err.message : String(err);\n          errors.push(`${file}: ${msg}`);\n\n          // Detect WASM runtime abort and attempt recovery\n          const isWasmCrash = (err as any)?.constructor?.name === 'RuntimeError'\n            || msg.includes('Aborted(') \n            || msg.includes('RuntimeError')\n            || msg.includes('WASM grammar exists but failed to load');\n          if (isWasmCrash) {\n            // Mark the language as poisoned so we skip remaining files of this language\n            const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n            const lang = detectLanguage(file);\n            poisonedLanguages.add(lang);\n\n            clearParserCache();\n            try {\n              await initGrammars();\n              // Recovery succeeded \u2014 un-poison all languages\n              poisonedLanguages.clear();\n            } catch {\n              errors.push('WASM runtime unrecoverable after crash \u2014 aborting batch');\n              break;\n            }\n          }\n        }\n      }\n\n      // Re-process files that have symbolCount=0 but should have symbols (WASM recovery)\n      const emptyFiles = this.db.getAllFiles().filter(\n        (f: any) => f.symbolCount === 0 && hasWasmGrammar(f.language)\n      );\n      if (emptyFiles.length > 0) {\n        opts?.onProgress?.({ phase: 'retrying', current: 0, total: emptyFiles.length });\n        for (let i = 0; i < emptyFiles.length; i++) {\n          const ef = emptyFiles[i];\n          const absPath = path.join(this.projectRoot, ef.path);\n          opts?.onProgress?.({ phase: 'retrying', current: i + 1, total: emptyFiles.length, currentFile: absPath });\n          try {\n            const extracted = await extractFile(absPath, this.projectRoot);\n            if (!extracted || extracted.nodes.length === 0) continue;\n\n            const oldNodes = this.db.getNodesByFile(extracted.filePath);\n            if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n            this.db.transaction(() => {\n              this.db.deleteNodesByFile(extracted.filePath);\n              this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n              this.db.upsertFile({\n                path: extracted.filePath,\n                contentHash: extracted.contentHash,\n                language: extracted.language,\n                fileSize: extracted.fileSize,\n                symbolCount: extracted.nodes.length,\n                indexedAt: Date.now(),\n              });\n              for (const node of extracted.nodes) { this.db.upsertNode(node); nodesCreated++; }\n              for (const edge of extracted.edges) { this.db.insertEdge(edge); edgesCreated++; }\n              for (const ref of extracted.unresolvedRefs) {\n                this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n              }\n            });\n            filesIndexed++;\n          } catch {\n            // Already logged in first pass or genuinely broken \u2014 skip\n          }\n        }\n      }\n\n      // Resolve cross-file references\n      opts?.onProgress?.({ phase: 'resolving', current: 0, total: 1 });\n      await this.resolver.resolveAll((current, total) => {\n        opts?.onProgress?.({ phase: 'resolving', current, total });\n      });\n\n      // Detect frameworks\n      opts?.onProgress?.({ phase: 'detecting frameworks', current: 0, total: 1 });\n      const detectedFrameworks = await detectFrameworks(this.projectRoot, this.db);\n      const languages = [...new Set(this.db.getAllFiles().map(f => (f as any).language).filter(Boolean))];\n      opts?.onProgress?.({\n        phase: 'detecting frameworks', current: 1, total: 1,\n        meta: { frameworks: detectedFrameworks.map(f => f.name), languages },\n      });\n\n      // Generate embeddings (if enabled)\n      if (this.vectors.isInitialized()) {\n        opts?.onProgress?.({ phase: 'embeddings', current: 0, total: 1 });\n        await this.vectors.embedAll((current, total) =>\n          opts?.onProgress?.({ phase: 'embeddings', current, total })\n        );\n      }\n\n      // Analyze architecture (if enabled, or auto-enabled for security)\n      if (this.config.enableArchitecture || this.config.enableSecurity) {\n        if (this.config.enableSecurity && !this.config.enableArchitecture) {\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          logWarn('enableSecurity requires enableArchitecture \u2014 auto-enabling architecture analysis for this run');\n        }\n        opts?.onProgress?.({ phase: 'architecture', current: 0, total: 1 });\n        await this.arch.analyze(msg =>\n          opts?.onProgress?.({ phase: 'architecture', current: 0, total: 1, meta: { msg } })\n        );\n        opts?.onProgress?.({ phase: 'architecture', current: 1, total: 1 });\n      }\n\n      // Run security analysis (if enabled)\n      if (this.config.enableSecurity) {\n        try {\n          const { SecurityPipeline } = await Promise.resolve().then(() => require('../security/pipeline.js'));\n          this.db.applySecuritySchema();\n          const secPipeline = new SecurityPipeline(this.db, this.config, this.projectRoot);\n          opts?.onProgress?.({ phase: 'security', current: 0, total: 1 });\n          await secPipeline.run((phase, current, total) =>\n            opts?.onProgress?.({ phase: 'security', current, total, meta: { secPhase: phase } })\n          );\n          opts?.onProgress?.({ phase: 'security', current: 1, total: 1 });\n        } catch { /* security analysis is non-critical */ }\n      }\n\n      // Index documentation (if enabled)\n      if (this.config.enableDocs) {\n        try {\n          const { DocsIndexer } = await Promise.resolve().then(() => require('../docs/indexer.js'));\n          this.db.applyDocsSchema();\n          const docsIndexer = new DocsIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await docsIndexer.indexAll({\n            force: opts?.force,\n            onProgress: msg => opts?.onProgress?.({ phase: 'docs', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\n      }\n\n      // Index data files (if enabled)\n      if ((this.config as any).enableData) {\n        try {\n          const { DataIndexer } = await Promise.resolve().then(() => require('../data/indexer.js'));\n          this.db.applyDataSchema();\n          const dataIndexer = new DataIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await dataIndexer.indexAll({\n            onProgress: msg => opts?.onProgress?.({ phase: 'data', current: 0, total: 1, meta: { msg } }),\n          });\n\n          // Assign data files to 'data' architecture layer if architecture is enabled\n          if (this.config.enableArchitecture) {\n            try {\n              const rawDb = this.db.getRawDb();\n              // Check if arch_file_layers table exists\n              const tableExists = rawDb.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='arch_file_layers'\");\n              if (tableExists) {\n                const datasets = rawDb.all('SELECT file_path FROM data_datasets') as Array<{ file_path: string }>;\n                for (const ds of datasets) {\n                  rawDb.run(\n                    `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence) VALUES (?, ?, ?)`,\n                    [ds.file_path, 'layer:data', 1.0],\n                  );\n                }\n              }\n            } catch { /* non-critical */ }\n          }\n        } catch { /* data indexing is non-critical */ }\n      }\n\n      // Index pattern matches (if enabled)\n      if ((this.config as any).enablePatterns) {\n        try {\n          this.db.applyPatternsSchema();\n          const { PatternIndexer } = await Promise.resolve().then(() => require('../patterns/indexer.js'));\n          const indexer = new PatternIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await indexer.indexAll((phase, current, total) => {\n            opts?.onProgress?.({ phase: 'patterns' as any, current, total });\n          });\n        } catch (err) {\n          // Patterns are non-critical \u2014 log and continue\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          const msg = err instanceof Error ? err.message : String(err);\n          logWarn(`[patterns] Pattern indexing failed (non-critical): ${msg}`);\n        }\n      }\n\n      this.lock.clearDirty();\n      return { success: errors.length === 0, filesIndexed, nodesCreated, edgesCreated, errors, duration: Date.now() - start };\n    } finally {\n      this.lock.release();\n      release();\n    }\n  }\n\n  async sync(opts?: {\n    changedFiles?: string[];\n    onProgress?: (p: IndexProgress) => void;\n  }): Promise<SyncResult> {\n    const release = await this.mutex.acquire();\n    this.lock.acquire();\n    const start = Date.now();\n    const changedFiles = opts?.changedFiles;\n    const onProgress = opts?.onProgress;\n    const result: SyncResult = {\n      added: [], modified: [], removed: [],\n      nodesCreated: 0, nodesUpdated: 0, nodesRemoved: 0,\n      edgesCreated: 0, edgesRemoved: 0,\n      filesScanned: 0, errors: [], duration: 0,\n    };\n\n    try {\n      const removeFile = async (rel: string) => {\n        const oldNodes = this.db.getNodesByFile(rel);\n        const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map(n => n.id)).length;\n        result.nodesRemoved += oldNodes.length;\n        result.edgesRemoved += oldEdgeCount;\n        await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n        this.db.deleteFile(rel);\n        this.db.deleteUnresolvedRefsByFile(rel);\n        // Clean up pattern matches for removed files\n        this.db.getRawDb().run('DELETE FROM pattern_matches WHERE file_path = ?', [rel]);\n        result.removed.push(rel);\n      };\n\n      // \u2500\u2500 Exclude-rule cleanup \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n      // Remove any indexed files that now match the current exclude patterns.\n      // This handles the case where a user adds a new exclude pattern (e.g.\n      // \"**/.vite/**\") and expects those files to disappear from the index on\n      // the next sync without needing a full --force re-index.\n      const allIndexed = this.db.getAllFiles();\n      for (const f of allIndexed) {\n        if (!shouldIncludeFile(f.path, this.config)) {\n          onProgress?.({ phase: 'scanning', current: 0, total: 0, meta: { excludeCleanup: true, file: f.path } });\n          await removeFile(f.path);\n        }\n      }\n\n      let filesToProcess: string[];\n\n      onProgress?.({ phase: 'scanning', current: 0, total: 0 });\n\n      if (changedFiles) {\n        filesToProcess = changedFiles.map(f => path.resolve(this.projectRoot, f));\n      } else {\n        const gitChanged = await getChangedFiles(this.projectRoot, this.config);\n        const hasChanges = gitChanged.added.length > 0 || gitChanged.modified.length > 0 || gitChanged.removed.length > 0;\n\n        if (hasChanges) {\n          for (const p of gitChanged.removed) {\n            await removeFile(path.relative(this.projectRoot, p).replace(/\\\\/g, '/'));\n          }\n          filesToProcess = [...gitChanged.added, ...gitChanged.modified];\n        } else {\n          // Fallback: full scan + detect removed files\n          const indexed = new Set(this.db.getAllFiles().map(f => f.path));\n          const current = new Set(\n            (await scanDirectory(this.projectRoot, this.config))\n              .map(f => path.relative(this.projectRoot, f).replace(/\\\\/g, '/'))\n          );\n          result.filesScanned = current.size;\n          for (const p of indexed) {\n            if (!current.has(p)) await removeFile(p);\n          }\n          filesToProcess = await scanDirectory(this.projectRoot, this.config);\n        }\n      }\n\n      result.filesScanned = result.filesScanned || filesToProcess.length;\n      onProgress?.({ phase: 'scanning', current: result.filesScanned, total: result.filesScanned });\n\n      const poisonedLanguages = new Set<string>();\n\n      for (let i = 0; i < filesToProcess.length; i++) {\n        const file = filesToProcess[i];\n        onProgress?.({ phase: 'parsing', current: i + 1, total: filesToProcess.length, currentFile: file });\n\n        if (!fs.existsSync(file)) {\n          const rel = path.relative(this.projectRoot, file).replace(/\\\\/g, '/');\n          await removeFile(rel);\n          continue;\n        }\n\n        try {\n          // Skip files whose language parser is currently poisoned\n          const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n          const lang = detectLanguage(file);\n          if (poisonedLanguages.has(lang)) continue;\n\n          const extracted = await extractFile(file, this.projectRoot);\n          if (!extracted) continue;\n\n          const existing = this.db.getFile(extracted.filePath);\n          const isNew = !existing;\n          if (!isNew && existing!.contentHash === extracted.contentHash) continue;\n\n          const oldNodes = this.db.getNodesByFile(extracted.filePath);\n          const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map(n => n.id)).length;\n          await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n          this.db.transaction(() => {\n            result.nodesRemoved += oldNodes.length;\n            result.edgesRemoved += oldEdgeCount;\n            this.db.deleteNodesByFile(extracted.filePath);\n            this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n            this.db.upsertFile({\n              path: extracted.filePath,\n              contentHash: extracted.contentHash,\n              language: extracted.language,\n              fileSize: extracted.fileSize,\n              symbolCount: extracted.nodes.length,\n              indexedAt: Date.now(),\n            });\n            for (const node of extracted.nodes) { this.db.upsertNode(node); result.nodesCreated++; }\n            for (const edge of extracted.edges) { this.db.insertEdge(edge); result.edgesCreated++; }\n            for (const ref of extracted.unresolvedRefs) {\n              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n            }\n          });\n\n          this.resolver.invalidateFile(extracted.filePath);\n          if (isNew) result.added.push(extracted.filePath);\n          else { result.modified.push(extracted.filePath); result.nodesUpdated += extracted.nodes.length; }\n        } catch (err) {\n          const msg = err instanceof Error ? err.message : String(err);\n          result.errors.push(`${file}: ${msg}`);\n\n          // Detect WASM runtime abort and attempt recovery\n          const isWasmCrash = (err as any)?.constructor?.name === 'RuntimeError'\n            || msg.includes('Aborted(') \n            || msg.includes('RuntimeError')\n            || msg.includes('WASM grammar exists but failed to load');\n          if (isWasmCrash) {\n            const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n            const lang = detectLanguage(file);\n            poisonedLanguages.add(lang);\n\n            clearParserCache();\n            try {\n              await initGrammars();\n              poisonedLanguages.clear();\n            } catch {\n              result.errors.push('WASM runtime unrecoverable after crash \u2014 aborting sync');\n              break;\n            }\n          }\n        }\n      }\n\n      // Resolve cross-file references\n      onProgress?.({ phase: 'resolving', current: 0, total: 1 });\n      await this.resolver.resolveAll((current, total) => {\n        onProgress?.({ phase: 'resolving', current, total });\n      });\n\n      await detectFrameworks(this.projectRoot);\n\n      // Generate embeddings (if enabled)\n      if (this.vectors.isInitialized()) {\n        onProgress?.({ phase: 'embeddings', current: 0, total: 1 });\n        await this.vectors.embedAll((current, total) =>\n          onProgress?.({ phase: 'embeddings', current, total })\n        );\n      }\n\n      // Analyze architecture (if enabled, or auto-enabled for security)\n      if (this.config.enableArchitecture || this.config.enableSecurity) {\n        if (this.config.enableSecurity && !this.config.enableArchitecture) {\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          logWarn('enableSecurity requires enableArchitecture \u2014 auto-enabling architecture analysis for this run');\n        }\n        onProgress?.({ phase: 'architecture', current: 0, total: 1 });\n        await this.arch.analyze(msg =>\n          onProgress?.({ phase: 'architecture', current: 0, total: 1, meta: { msg } })\n        );\n        onProgress?.({ phase: 'architecture', current: 1, total: 1 });\n      }\n\n      // Run security analysis (if enabled)\n      if (this.config.enableSecurity) {\n        try {\n          const { SecurityPipeline } = await Promise.resolve().then(() => require('../security/pipeline.js'));\n          this.db.applySecuritySchema();\n          const secPipeline = new SecurityPipeline(this.db, this.config, this.projectRoot);\n          onProgress?.({ phase: 'security', current: 0, total: 1 });\n          await secPipeline.run((phase, current, total) =>\n            onProgress?.({ phase: 'security', current, total, meta: { secPhase: phase } })\n          );\n          onProgress?.({ phase: 'security', current: 1, total: 1 });\n        } catch { /* security analysis is non-critical */ }\n      }\n\n      // Re-index documentation (if enabled)\n      if (this.config.enableDocs) {\n        try {\n          const { DocsIndexer } = await Promise.resolve().then(() => require('../docs/indexer.js'));\n          this.db.applyDocsSchema();\n          const docsIndexer = new DocsIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await docsIndexer.indexAll({\n            onProgress: msg => onProgress?.({ phase: 'docs', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\n      }\n\n      // Re-index data files (if enabled)\n      if ((this.config as any).enableData) {\n        try {\n          const { DataIndexer } = await Promise.resolve().then(() => require('../data/indexer.js'));\n          this.db.applyDataSchema();\n          const dataIndexer = new DataIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await dataIndexer.indexAll({\n            onProgress: msg => onProgress?.({ phase: 'data', current: 0, total: 1, meta: { msg } }),\n          });\n\n          // Assign data files to 'data' architecture layer if architecture is enabled\n          if (this.config.enableArchitecture) {\n            try {\n              const rawDb = this.db.getRawDb();\n              const tableExists = rawDb.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='arch_file_layers'\");\n              if (tableExists) {\n                const datasets = rawDb.all('SELECT file_path FROM data_datasets') as Array<{ file_path: string }>;\n                for (const ds of datasets) {\n                  rawDb.run(\n                    `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence) VALUES (?, ?, ?)`,\n                    [ds.file_path, 'layer:data', 1.0],\n                  );\n                }\n              }\n            } catch { /* non-critical */ }\n          }\n        } catch { /* data indexing is non-critical */ }\n      }\n\n      // Re-index pattern matches for changed files (if enabled)\n      if ((this.config as any).enablePatterns) {\n        try {\n          const tableExists = this.db.getRawDb().get(\n            \"SELECT name FROM sqlite_master WHERE type='table' AND name='pattern_matches'\"\n          );\n          if (tableExists) {\n            const { PatternIndexer } = await Promise.resolve().then(() => require('../patterns/indexer.js'));\n            const { PatternLibraryLoader } = await Promise.resolve().then(() => require('../patterns/loader.js'));\n            const { PatternRunner } = await Promise.resolve().then(() => require('../patterns/runner.js'));\n            const runner = new PatternRunner();\n            if (runner.isAvailable()) {\n              const loader = new PatternLibraryLoader();\n              const builtinPath = require('path').join(__dirname, '../patterns/library');\n              const rules = loader.load(builtinPath, (this.config as any).patternLibraryPath);\n              const threshold = (this.config as any).patternSeverityThreshold ?? 'low';\n              const indexer = new PatternIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n              const changedPaths = [...result.added, ...result.modified];\n              for (const filePath of changedPaths) {\n                const fileRecord = this.db.getFile(filePath);\n                const language = fileRecord?.language ?? 'unknown';\n                await indexer.indexFile(filePath, language, rules, runner, threshold, Date.now());\n              }\n            }\n          }\n        } catch { /* non-critical */ }\n      }\n\n      this.lock.clearDirty();\n      result.duration = Date.now() - start;\n      return result;\n    } finally {\n      this.lock.release();\n      release();\n    }\n  }\n}\n"],
-  "mappings": 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+  "sourcesContent": ["/**\n * IndexPipeline \u2014 full-index and incremental-sync pipelines.\n *\n * Owns the two heavy workflows:\n *   - indexAll(): scan all files, extract, store, resolve, detect frameworks,\n *                 generate embeddings, analyze architecture.\n *   - sync():     detect changed files via git (or full scan fallback),\n *                 re-extract only what changed, then run the same tail pipeline.\n *\n * Everything that touches the filesystem or sub-systems is injected via the\n * constructor, keeping this class testable and free of global state.\n */\n\nimport * as path from 'path';\nimport * as fs from 'fs';\nimport { GraphDatabase } from '../db/database';\nimport { scanDirectory, hashContent, getChangedFiles, shouldIncludeFile } from '../sync/index';\nimport { extractFile } from '../extraction/extractor';\nimport { clearParserCache, initGrammars, hasWasmGrammar } from '../extraction/grammars';\nimport { detectFrameworks } from '../frameworks/index';\nimport { ReferenceResolver } from '../resolution/index';\nimport { VectorManager } from '../vectors/index';\nimport { ArchitectureAnalyzer } from '../architecture/index';\nimport type { KiroGraphConfig } from '../config';\nimport type { IndexResult, IndexProgress, SyncResult } from '../types';\nimport { LockManager } from './lock-manager';\nimport { Mutex } from '../utils';\n\nconst FILE_IO_BATCH_SIZE = 10;\n\nexport class IndexPipeline {\n  private readonly mutex = new Mutex();\n\n  constructor(\n    private readonly db: GraphDatabase,\n    private readonly vectors: VectorManager,\n    private readonly resolver: ReferenceResolver,\n    private readonly arch: ArchitectureAnalyzer,\n    private readonly lock: LockManager,\n    private readonly config: KiroGraphConfig,\n    private readonly projectRoot: string,\n  ) {}\n\n  async indexAll(opts?: {\n    onProgress?: (p: IndexProgress) => void;\n    force?: boolean;\n    signal?: AbortSignal;\n  }): Promise<IndexResult> {\n    const release = await this.mutex.acquire();\n    this.lock.acquire();\n    const start = Date.now();\n    const errors: string[] = [];\n    let filesIndexed = 0;\n    let nodesCreated = 0;\n    let edgesCreated = 0;\n\n    // Track languages whose WASM parser is currently poisoned (ABORT=true on the module).\n    // Once a language's parser aborts, every subsequent parse call for that language\n    // fails instantly. We skip those files until clearParserCache + initGrammars succeeds.\n    const poisonedLanguages = new Set<string>();\n\n    try {\n      const files = await scanDirectory(this.projectRoot, this.config, opts?.signal);\n      opts?.onProgress?.({ phase: 'scanning', current: files.length, total: files.length });\n\n      // Batch-read files in parallel\n      const contentMap = new Map<string, Buffer>();\n      for (let b = 0; b < files.length; b += FILE_IO_BATCH_SIZE) {\n        const batch = files.slice(b, b + FILE_IO_BATCH_SIZE);\n        const results = await Promise.all(batch.map(f => fs.promises.readFile(f).catch(() => null)));\n        for (let i = 0; i < batch.length; i++) {\n          if (results[i]) contentMap.set(batch[i], results[i]!);\n        }\n      }\n\n      for (let i = 0; i < files.length; i++) {\n        const file = files[i];\n        opts?.onProgress?.({ phase: 'parsing', current: i + 1, total: files.length, currentFile: file });\n\n        try {\n          const content = contentMap.get(file);\n          if (!content) continue;\n          if (content.length > this.config.maxFileSize) continue;\n\n          const relPath = path.relative(this.projectRoot, file).replace(/\\\\/g, '/');\n\n          if (!opts?.force) {\n            const existing = this.db.getFile(relPath);\n            if (existing && hashContent(content) === existing.contentHash) continue;\n          }\n\n          // Skip files whose language parser is currently poisoned\n          const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n          const lang = detectLanguage(file);\n          if (poisonedLanguages.has(lang)) continue;\n\n          const extracted = await extractFile(file, this.projectRoot, content);\n          if (!extracted) continue;\n\n          const oldNodes = this.db.getNodesByFile(extracted.filePath);\n          if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n          this.db.transaction(() => {\n            this.db.deleteNodesByFile(extracted.filePath);\n            this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n            this.db.upsertFile({\n              path: extracted.filePath,\n              contentHash: extracted.contentHash,\n              language: extracted.language,\n              fileSize: extracted.fileSize,\n              symbolCount: extracted.nodes.length,\n              indexedAt: Date.now(),\n            });\n            for (const node of extracted.nodes) { this.db.upsertNode(node); nodesCreated++; }\n            for (const edge of extracted.edges) { this.db.insertEdge(edge); edgesCreated++; }\n            for (const ref of extracted.unresolvedRefs) {\n              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n            }\n          });\n\n          filesIndexed++;\n        } catch (err) {\n          const msg = err instanceof Error ? err.message : String(err);\n          errors.push(`${file}: ${msg}`);\n\n          // Detect WASM runtime abort and attempt recovery\n          const isWasmCrash = (err as any)?.constructor?.name === 'RuntimeError'\n            || msg.includes('Aborted(') \n            || msg.includes('RuntimeError')\n            || msg.includes('WASM grammar exists but failed to load');\n          if (isWasmCrash) {\n            // Mark the language as poisoned so we skip remaining files of this language\n            const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n            const lang = detectLanguage(file);\n            poisonedLanguages.add(lang);\n\n            clearParserCache();\n            try {\n              await initGrammars();\n              // Recovery succeeded \u2014 un-poison all languages\n              poisonedLanguages.clear();\n            } catch {\n              errors.push('WASM runtime unrecoverable after crash \u2014 aborting batch');\n              break;\n            }\n          }\n        }\n      }\n\n      // Re-process files that have symbolCount=0 but should have symbols (WASM recovery)\n      const emptyFiles = this.db.getAllFiles().filter(\n        (f: any) => f.symbolCount === 0 && hasWasmGrammar(f.language)\n      );\n      if (emptyFiles.length > 0) {\n        opts?.onProgress?.({ phase: 'retrying', current: 0, total: emptyFiles.length });\n        for (let i = 0; i < emptyFiles.length; i++) {\n          const ef = emptyFiles[i];\n          const absPath = path.join(this.projectRoot, ef.path);\n          opts?.onProgress?.({ phase: 'retrying', current: i + 1, total: emptyFiles.length, currentFile: absPath });\n          try {\n            const extracted = await extractFile(absPath, this.projectRoot);\n            if (!extracted || extracted.nodes.length === 0) continue;\n\n            const oldNodes = this.db.getNodesByFile(extracted.filePath);\n            if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n            this.db.transaction(() => {\n              this.db.deleteNodesByFile(extracted.filePath);\n              this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n              this.db.upsertFile({\n                path: extracted.filePath,\n                contentHash: extracted.contentHash,\n                language: extracted.language,\n                fileSize: extracted.fileSize,\n                symbolCount: extracted.nodes.length,\n                indexedAt: Date.now(),\n              });\n              for (const node of extracted.nodes) { this.db.upsertNode(node); nodesCreated++; }\n              for (const edge of extracted.edges) { this.db.insertEdge(edge); edgesCreated++; }\n              for (const ref of extracted.unresolvedRefs) {\n                this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n              }\n            });\n            filesIndexed++;\n          } catch {\n            // Already logged in first pass or genuinely broken \u2014 skip\n          }\n        }\n      }\n\n      // Resolve cross-file references\n      opts?.onProgress?.({ phase: 'resolving', current: 0, total: 1 });\n      await this.resolver.resolveAll((current, total) => {\n        opts?.onProgress?.({ phase: 'resolving', current, total });\n      });\n\n      // Detect frameworks\n      opts?.onProgress?.({ phase: 'detecting frameworks', current: 0, total: 1 });\n      const detectedFrameworks = await detectFrameworks(this.projectRoot, this.db);\n      const languages = [...new Set(this.db.getAllFiles().map(f => (f as any).language).filter(Boolean))];\n      opts?.onProgress?.({\n        phase: 'detecting frameworks', current: 1, total: 1,\n        meta: { frameworks: detectedFrameworks.map(f => f.name), languages },\n      });\n\n      // Generate embeddings (if enabled)\n      if (this.vectors.isInitialized()) {\n        opts?.onProgress?.({ phase: 'embeddings', current: 0, total: 1 });\n        await this.vectors.embedAll((current, total) =>\n          opts?.onProgress?.({ phase: 'embeddings', current, total })\n        );\n      }\n\n      // Analyze architecture (if enabled, or auto-enabled for security)\n      if (this.config.enableArchitecture || this.config.enableSecurity) {\n        if (this.config.enableSecurity && !this.config.enableArchitecture) {\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          logWarn('enableSecurity requires enableArchitecture \u2014 auto-enabling architecture analysis for this run');\n        }\n        opts?.onProgress?.({ phase: 'architecture', current: 0, total: 1 });\n        await this.arch.analyze(msg =>\n          opts?.onProgress?.({ phase: 'architecture', current: 0, total: 1, meta: { msg } })\n        );\n        opts?.onProgress?.({ phase: 'architecture', current: 1, total: 1 });\n      }\n\n      // Run security analysis (if enabled)\n      if (this.config.enableSecurity) {\n        try {\n          const { SecurityPipeline } = await Promise.resolve().then(() => require('../security/pipeline.js'));\n          this.db.applySecuritySchema();\n          const secPipeline = new SecurityPipeline(this.db, this.config, this.projectRoot);\n          opts?.onProgress?.({ phase: 'security', current: 0, total: 1 });\n          await secPipeline.run((phase, current, total) =>\n            opts?.onProgress?.({ phase: 'security', current, total, meta: { secPhase: phase } })\n          );\n          opts?.onProgress?.({ phase: 'security', current: 1, total: 1 });\n        } catch { /* security analysis is non-critical */ }\n      }\n\n      // Index documentation (if enabled)\n      if (this.config.enableDocs) {\n        try {\n          const { DocsIndexer } = await Promise.resolve().then(() => require('../docs/indexer.js'));\n          this.db.applyDocsSchema();\n          const docsIndexer = new DocsIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await docsIndexer.indexAll({\n            force: opts?.force,\n            onProgress: msg => opts?.onProgress?.({ phase: 'docs', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\n      }\n\n      // Index data files (if enabled)\n      if ((this.config as any).enableData) {\n        try {\n          const { DataIndexer } = await Promise.resolve().then(() => require('../data/indexer.js'));\n          this.db.applyDataSchema();\n          const dataIndexer = new DataIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await dataIndexer.indexAll({\n            onProgress: msg => opts?.onProgress?.({ phase: 'data', current: 0, total: 1, meta: { msg } }),\n          });\n\n          // Assign data files to 'data' architecture layer if architecture is enabled\n          if (this.config.enableArchitecture) {\n            try {\n              const rawDb = this.db.getRawDb();\n              // Check if arch_file_layers table exists\n              const tableExists = rawDb.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='arch_file_layers'\");\n              if (tableExists) {\n                const datasets = rawDb.all('SELECT file_path FROM data_datasets') as Array<{ file_path: string }>;\n                for (const ds of datasets) {\n                  rawDb.run(\n                    `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence) VALUES (?, ?, ?)`,\n                    [ds.file_path, 'layer:data', 1.0],\n                  );\n                }\n              }\n            } catch { /* non-critical */ }\n          }\n        } catch { /* data indexing is non-critical */ }\n      }\n\n      // Index pattern matches (if enabled)\n      if ((this.config as any).enablePatterns) {\n        try {\n          this.db.applyPatternsSchema();\n          const { PatternIndexer } = await Promise.resolve().then(() => require('../patterns/indexer.js'));\n          const indexer = new PatternIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await indexer.indexAll((phase, current, total) => {\n            opts?.onProgress?.({ phase: 'patterns' as any, current, total });\n          });\n        } catch (err) {\n          // Patterns are non-critical \u2014 log and continue\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          const msg = err instanceof Error ? err.message : String(err);\n          logWarn(`[patterns] Pattern indexing failed (non-critical): ${msg}`);\n        }\n      }\n\n      this.lock.clearDirty();\n      return { success: errors.length === 0, filesIndexed, nodesCreated, edgesCreated, errors, duration: Date.now() - start };\n    } finally {\n      this.lock.release();\n      release();\n    }\n  }\n\n  async sync(opts?: {\n    changedFiles?: string[];\n    onProgress?: (p: IndexProgress) => void;\n  }): Promise<SyncResult> {\n    const release = await this.mutex.acquire();\n    this.lock.acquire();\n    const start = Date.now();\n    const changedFiles = opts?.changedFiles;\n    const onProgress = opts?.onProgress;\n    const result: SyncResult = {\n      added: [], modified: [], removed: [],\n      nodesCreated: 0, nodesUpdated: 0, nodesRemoved: 0,\n      edgesCreated: 0, edgesRemoved: 0,\n      filesScanned: 0, errors: [], duration: 0,\n    };\n\n    try {\n      const removeFile = async (rel: string) => {\n        const oldNodes = this.db.getNodesByFile(rel);\n        const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map(n => n.id)).length;\n        result.nodesRemoved += oldNodes.length;\n        result.edgesRemoved += oldEdgeCount;\n        await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n        this.db.deleteFile(rel);\n        this.db.deleteUnresolvedRefsByFile(rel);\n        // Clean up pattern matches for removed files (only if patterns are enabled)\n        if ((this.config as any).enablePatterns) {\n          this.db.getRawDb().run('DELETE FROM pattern_matches WHERE file_path = ?', [rel]);\n        }\n        result.removed.push(rel);\n      };\n\n      // \u2500\u2500 Exclude-rule cleanup \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n      // Remove any indexed files that now match the current exclude patterns.\n      // This handles the case where a user adds a new exclude pattern (e.g.\n      // \"**/.vite/**\") and expects those files to disappear from the index on\n      // the next sync without needing a full --force re-index.\n      const allIndexed = this.db.getAllFiles();\n      for (const f of allIndexed) {\n        if (!shouldIncludeFile(f.path, this.config)) {\n          onProgress?.({ phase: 'scanning', current: 0, total: 0, meta: { excludeCleanup: true, file: f.path } });\n          await removeFile(f.path);\n        }\n      }\n\n      let filesToProcess: string[];\n\n      onProgress?.({ phase: 'scanning', current: 0, total: 0 });\n\n      if (changedFiles) {\n        filesToProcess = changedFiles.map(f => path.resolve(this.projectRoot, f));\n      } else {\n        const gitChanged = await getChangedFiles(this.projectRoot, this.config);\n        const hasChanges = gitChanged.added.length > 0 || gitChanged.modified.length > 0 || gitChanged.removed.length > 0;\n\n        if (hasChanges) {\n          for (const p of gitChanged.removed) {\n            await removeFile(path.relative(this.projectRoot, p).replace(/\\\\/g, '/'));\n          }\n          filesToProcess = [...gitChanged.added, ...gitChanged.modified];\n        } else {\n          // Fallback: full scan + detect removed files\n          const indexed = new Set(this.db.getAllFiles().map(f => f.path));\n          const current = new Set(\n            (await scanDirectory(this.projectRoot, this.config))\n              .map(f => path.relative(this.projectRoot, f).replace(/\\\\/g, '/'))\n          );\n          result.filesScanned = current.size;\n          for (const p of indexed) {\n            if (!current.has(p)) await removeFile(p);\n          }\n          filesToProcess = await scanDirectory(this.projectRoot, this.config);\n        }\n      }\n\n      result.filesScanned = result.filesScanned || filesToProcess.length;\n      onProgress?.({ phase: 'scanning', current: result.filesScanned, total: result.filesScanned });\n\n      const poisonedLanguages = new Set<string>();\n\n      for (let i = 0; i < filesToProcess.length; i++) {\n        const file = filesToProcess[i];\n        onProgress?.({ phase: 'parsing', current: i + 1, total: filesToProcess.length, currentFile: file });\n\n        if (!fs.existsSync(file)) {\n          const rel = path.relative(this.projectRoot, file).replace(/\\\\/g, '/');\n          await removeFile(rel);\n          continue;\n        }\n\n        try {\n          // Skip files whose language parser is currently poisoned\n          const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n          const lang = detectLanguage(file);\n          if (poisonedLanguages.has(lang)) continue;\n\n          const extracted = await extractFile(file, this.projectRoot);\n          if (!extracted) continue;\n\n          const existing = this.db.getFile(extracted.filePath);\n          const isNew = !existing;\n          if (!isNew && existing!.contentHash === extracted.contentHash) continue;\n\n          const oldNodes = this.db.getNodesByFile(extracted.filePath);\n          const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map(n => n.id)).length;\n          await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n          this.db.transaction(() => {\n            result.nodesRemoved += oldNodes.length;\n            result.edgesRemoved += oldEdgeCount;\n            this.db.deleteNodesByFile(extracted.filePath);\n            this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n            this.db.upsertFile({\n              path: extracted.filePath,\n              contentHash: extracted.contentHash,\n              language: extracted.language,\n              fileSize: extracted.fileSize,\n              symbolCount: extracted.nodes.length,\n              indexedAt: Date.now(),\n            });\n            for (const node of extracted.nodes) { this.db.upsertNode(node); result.nodesCreated++; }\n            for (const edge of extracted.edges) { this.db.insertEdge(edge); result.edgesCreated++; }\n            for (const ref of extracted.unresolvedRefs) {\n              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n            }\n          });\n\n          this.resolver.invalidateFile(extracted.filePath);\n          if (isNew) result.added.push(extracted.filePath);\n          else { result.modified.push(extracted.filePath); result.nodesUpdated += extracted.nodes.length; }\n        } catch (err) {\n          const msg = err instanceof Error ? err.message : String(err);\n          result.errors.push(`${file}: ${msg}`);\n\n          // Detect WASM runtime abort and attempt recovery\n          const isWasmCrash = (err as any)?.constructor?.name === 'RuntimeError'\n            || msg.includes('Aborted(') \n            || msg.includes('RuntimeError')\n            || msg.includes('WASM grammar exists but failed to load');\n          if (isWasmCrash) {\n            const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n            const lang = detectLanguage(file);\n            poisonedLanguages.add(lang);\n\n            clearParserCache();\n            try {\n              await initGrammars();\n              poisonedLanguages.clear();\n            } catch {\n              result.errors.push('WASM runtime unrecoverable after crash \u2014 aborting sync');\n              break;\n            }\n          }\n        }\n      }\n\n      // Resolve cross-file references\n      onProgress?.({ phase: 'resolving', current: 0, total: 1 });\n      await this.resolver.resolveAll((current, total) => {\n        onProgress?.({ phase: 'resolving', current, total });\n      });\n\n      await detectFrameworks(this.projectRoot);\n\n      // Generate embeddings (if enabled)\n      if (this.vectors.isInitialized()) {\n        onProgress?.({ phase: 'embeddings', current: 0, total: 1 });\n        await this.vectors.embedAll((current, total) =>\n          onProgress?.({ phase: 'embeddings', current, total })\n        );\n      }\n\n      // Analyze architecture (if enabled, or auto-enabled for security)\n      if (this.config.enableArchitecture || this.config.enableSecurity) {\n        if (this.config.enableSecurity && !this.config.enableArchitecture) {\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          logWarn('enableSecurity requires enableArchitecture \u2014 auto-enabling architecture analysis for this run');\n        }\n        onProgress?.({ phase: 'architecture', current: 0, total: 1 });\n        await this.arch.analyze(msg =>\n          onProgress?.({ phase: 'architecture', current: 0, total: 1, meta: { msg } })\n        );\n        onProgress?.({ phase: 'architecture', current: 1, total: 1 });\n      }\n\n      // Run security analysis (if enabled)\n      if (this.config.enableSecurity) {\n        try {\n          const { SecurityPipeline } = await Promise.resolve().then(() => require('../security/pipeline.js'));\n          this.db.applySecuritySchema();\n          const secPipeline = new SecurityPipeline(this.db, this.config, this.projectRoot);\n          onProgress?.({ phase: 'security', current: 0, total: 1 });\n          await secPipeline.run((phase, current, total) =>\n            onProgress?.({ phase: 'security', current, total, meta: { secPhase: phase } })\n          );\n          onProgress?.({ phase: 'security', current: 1, total: 1 });\n        } catch { /* security analysis is non-critical */ }\n      }\n\n      // Re-index documentation (if enabled)\n      if (this.config.enableDocs) {\n        try {\n          const { DocsIndexer } = await Promise.resolve().then(() => require('../docs/indexer.js'));\n          this.db.applyDocsSchema();\n          const docsIndexer = new DocsIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await docsIndexer.indexAll({\n            onProgress: msg => onProgress?.({ phase: 'docs', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\n      }\n\n      // Re-index data files (if enabled)\n      if ((this.config as any).enableData) {\n        try {\n          const { DataIndexer } = await Promise.resolve().then(() => require('../data/indexer.js'));\n          this.db.applyDataSchema();\n          const dataIndexer = new DataIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await dataIndexer.indexAll({\n            onProgress: msg => onProgress?.({ phase: 'data', current: 0, total: 1, meta: { msg } }),\n          });\n\n          // Assign data files to 'data' architecture layer if architecture is enabled\n          if (this.config.enableArchitecture) {\n            try {\n              const rawDb = this.db.getRawDb();\n              const tableExists = rawDb.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='arch_file_layers'\");\n              if (tableExists) {\n                const datasets = rawDb.all('SELECT file_path FROM data_datasets') as Array<{ file_path: string }>;\n                for (const ds of datasets) {\n                  rawDb.run(\n                    `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence) VALUES (?, ?, ?)`,\n                    [ds.file_path, 'layer:data', 1.0],\n                  );\n                }\n              }\n            } catch { /* non-critical */ }\n          }\n        } catch { /* data indexing is non-critical */ }\n      }\n\n      // Re-index pattern matches for changed files (if enabled)\n      if ((this.config as any).enablePatterns) {\n        try {\n          const tableExists = this.db.getRawDb().get(\n            \"SELECT name FROM sqlite_master WHERE type='table' AND name='pattern_matches'\"\n          );\n          if (tableExists) {\n            const { PatternIndexer } = await Promise.resolve().then(() => require('../patterns/indexer.js'));\n            const { PatternLibraryLoader } = await Promise.resolve().then(() => require('../patterns/loader.js'));\n            const { PatternRunner } = await Promise.resolve().then(() => require('../patterns/runner.js'));\n            const runner = new PatternRunner();\n            if (runner.isAvailable()) {\n              const loader = new PatternLibraryLoader();\n              const builtinPath = require('path').join(__dirname, '../patterns/library');\n              const rules = loader.load(builtinPath, (this.config as any).patternLibraryPath);\n              const threshold = (this.config as any).patternSeverityThreshold ?? 'low';\n              const indexer = new PatternIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n              const changedPaths = [...result.added, ...result.modified];\n              for (const filePath of changedPaths) {\n                const fileRecord = this.db.getFile(filePath);\n                const language = fileRecord?.language ?? 'unknown';\n                await indexer.indexFile(filePath, language, rules, runner, threshold, Date.now());\n              }\n            }\n          }\n        } catch { /* non-critical */ }\n      }\n\n      this.lock.clearDirty();\n      result.duration = Date.now() - start;\n      return result;\n    } finally {\n      this.lock.release();\n      release();\n    }\n  }\n}\n"],
+  "mappings": 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   "names": []
 }

package/dist/data/indexer.js

@@ -99,7 +99,7 @@ class DataIndexer {
     const profiler = new import_profiler.ColumnProfiler();
     const allRows = [];
     const maxRows = this.config.dataMaxRows ?? 1e6;
-    const { columns, totalRows } = await parser.parse(absPath, {
+    const { columns, totalRows, metadataJson } = await parser.parse(absPath, {
       maxRows,
       onBatch: (rows, cols) => {
         profiler.addBatch(rows, cols);
@@ -115,9 +115,9 @@ class DataIndexer {
       this.db.run("DELETE FROM data_columns WHERE dataset_id = ?", [datasetId]);
       this.db.run("DELETE FROM data_datasets WHERE id = ?", [datasetId]);
       this.db.run(`
-        INSERT INTO data_datasets (id, file_path, format, row_count, column_count, file_size, content_hash, summary, indexed_at)
-        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
-      `, [datasetId, relPath, parser.name, totalRows, columns.length, stat.size, contentHash, null, Date.now()]);
+        INSERT INTO data_datasets (id, file_path, format, row_count, column_count, file_size, content_hash, summary, indexed_at, metadata_json)
+        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+      `, [datasetId, relPath, parser.name, totalRows, columns.length, stat.size, contentHash, null, Date.now(), metadataJson ?? null]);
       for (const col of columnProfiles) {
         this.db.run(`
           INSERT INTO data_columns (id, dataset_id, name, position, inferred_type, nullable, null_count, null_pct, cardinality, min_value, max_value, mean_value, sample_values, summary, updated_at)