kirograph 0.20.0 → 0.20.1

package/dist/patterns/runner.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/patterns/runner.ts"],
-  "sourcesContent": ["/**\n * KiroGraph PatternRunner \u2014 lazy-loads @ast-grep/napi and executes pattern rules.\n */\n\nimport { PatternRule, PatternMatch, SEVERITY_ORDER } from './types';\nimport { logWarn } from '../errors';\n\n// Languages supported by @ast-grep/napi tree-sitter grammars.\n// Calling parse() with an unsupported language throws a native C++ exception\n// that bypasses JS try/catch and corrupts the mutex \u2014 skip unsupported languages.\nconst NAPI_SUPPORTED_LANGUAGES = new Set([\n  'javascript', 'typescript', 'tsx', 'jsx',\n  'python', 'go', 'rust', 'java', 'c', 'cpp', 'cs', 'swift', 'kotlin',\n  'html', 'css', 'json', 'yaml', 'bash', 'ruby', 'php', 'scala',\n  'haskell', 'lua', 'r', 'dart', 'elixir', 'erlang', 'ocaml',\n]);\n\n// Module-level cache: undefined = not yet attempted, null = missing, module = loaded\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nlet _napi: any | null | undefined = undefined;\nlet _napiWarnLogged = false;\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nasync function getNapi(): Promise<any | null> {\n  if (_napi !== undefined) return _napi;\n  try {\n    // Verify it can be resolved synchronously before async import\n    require.resolve('@ast-grep/napi');\n    // eslint-disable-next-line @typescript-eslint/no-require-imports\n    _napi = require('@ast-grep/napi');\n    return _napi;\n  } catch {\n    _napi = null;\n    if (!_napiWarnLogged) {\n      logWarn('PatternRunner: @ast-grep/napi is not installed. Pattern matching is disabled. Run: npm install @ast-grep/napi');\n      _napiWarnLogged = true;\n    }\n    return null;\n  }\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction renderFix(fixTemplate: string, node: any): string | undefined {\n  if (!fixTemplate) return undefined;\n  // Replace $VAR metavariables with matched text\n  return fixTemplate.replace(/\\$([A-Z_]+)/g, (_, varName) => {\n    try {\n      return node.getMatch(varName)?.text() ?? `$${varName}`;\n    } catch {\n      return `$${varName}`;\n    }\n  });\n}\n\nexport class PatternRunner {\n  /**\n   * Synchronously check whether @ast-grep/napi is available.\n   */\n  isAvailable(): boolean {\n    try {\n      require.resolve('@ast-grep/napi');\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Returns true if the language is supported by @ast-grep/napi.\n   * Unsupported languages must be skipped \u2014 calling parse() on them throws a\n   * native C++ exception that bypasses JS try/catch and corrupts internal mutexes.\n   */\n  isSupportedLanguage(language: string): boolean {\n    return NAPI_SUPPORTED_LANGUAGES.has(language.toLowerCase());\n  }\n\n  /**\n   * Lazy async loader \u2014 returns the napi module or null if missing.\n   */\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  async getNapi(): Promise<any | null> {\n    return getNapi();\n  }\n\n  /**\n   * Run a single library rule against a file's content.\n   * Returns an empty array and logs a warning on per-file errors.\n   */\n  async runRule(rule: PatternRule, fileContent: string, language: string): Promise<PatternMatch[]> {\n    if (!this.isSupportedLanguage(language)) return [];\n    const napi = await getNapi();\n    if (!napi) return [];\n\n    try {\n      const { parse } = napi;\n      const root = parse(language as any, fileContent);\n      const nodes = root.root().findAll({ rule: rule.rule as any });\n      const lines = fileContent.split('\\n');\n\n      // eslint-disable-next-line @typescript-eslint/no-explicit-any\n      return nodes.map((node: any) => {\n        const range = node.range();\n        const line = range.start.line + 1; // 1-based\n        const col = range.start.column;    // 0-based\n        const matchText = node.text().slice(0, 500);\n        const context = _buildContext(lines, range.start.line);\n        const fixSuggestion = rule.fix ? renderFix(rule.fix, node) : undefined;\n\n        return {\n          patternId: rule.id,\n          filePath: '',\n          line,\n          col,\n          matchText,\n          context,\n          severity: rule.severity,\n          owaspCategory: rule.owaspCategory,\n          language,\n          ...(fixSuggestion !== undefined ? { fixSuggestion } : {}),\n        };\n      });\n    } catch (err) {\n      logWarn(`PatternRunner: error running rule \"${rule.id}\" on file (language: ${language}): ${err instanceof Error ? err.message : String(err)}`);\n      return [];\n    }\n  }\n\n  /**\n   * Run an inline pattern expression (not from library) against file content.\n   * Returns an empty array and logs a warning on per-file errors.\n   */\n  async runInline(pattern: string, language: string, fileContent: string): Promise<PatternMatch[]> {\n    if (!this.isSupportedLanguage(language)) return [];\n    const napi = await getNapi();\n    if (!napi) return [];\n\n    try {\n      const { parse } = napi;\n      const root = parse(language as any, fileContent);\n      const nodes = root.root().findAll(pattern);\n      const lines = fileContent.split('\\n');\n\n      // eslint-disable-next-line @typescript-eslint/no-explicit-any\n      return nodes.map((node: any) => {\n        const range = node.range();\n        const line = range.start.line + 1;\n        const col = range.start.column;\n        const matchText = node.text().slice(0, 500);\n        const context = _buildContext(lines, range.start.line);\n\n        return {\n          patternId: '',\n          filePath: '',\n          line,\n          col,\n          matchText,\n          context,\n          severity: 'low' as const,\n          owaspCategory: '',\n          language,\n        };\n      });\n    } catch (err) {\n      logWarn(`PatternRunner: error running inline pattern on file (language: ${language}): ${err instanceof Error ? err.message : String(err)}`);\n      return [];\n    }\n  }\n\n  /**\n   * Run all rules against a file's content, filtered by severity threshold.\n   */\n  async runAllRules(\n    rules: PatternRule[],\n    fileContent: string,\n    language: string,\n    threshold: PatternRule['severity'],\n  ): Promise<PatternMatch[]> {\n    const napi = await getNapi();\n    if (!napi) return [];\n\n    const thresholdOrder = SEVERITY_ORDER[threshold];\n    const applicableRules = rules.filter(r => {\n      const langs = Array.isArray(r.language) ? r.language : [r.language];\n      return langs.includes(language) && SEVERITY_ORDER[r.severity] >= thresholdOrder;\n    });\n\n    const results: PatternMatch[] = [];\n    for (const rule of applicableRules) {\n      const matches = await this.runRule(rule, fileContent, language);\n      results.push(...matches);\n    }\n    return results;\n  }\n\n  /**\n   * Apply the rule's fix template to all matches in the file content.\n   * Returns the transformed source string, or null if no fix was applied.\n   * Uses a range-based text substitution approach since commitEdits may not\n   * be available in all versions of @ast-grep/napi.\n   */\n  async applyFix(filePath: string, fileContent: string, language: string, rule: PatternRule): Promise<string | null> {\n    const napi = await this.getNapi();\n    if (!napi || !rule.fix) return null;\n    try {\n      const { parse } = napi;\n      const root = parse(language as any, fileContent);\n      const nodes = root.root().findAll({ rule: rule.rule as any });\n      if (nodes.length === 0) return null;\n\n      // Try the native commitEdits API first\n      try {\n        // eslint-disable-next-line @typescript-eslint/no-explicit-any\n        for (const node of nodes as any[]) {\n          const fixText = renderFix(rule.fix, node);\n          if (fixText) node.replace(fixText);\n        }\n        // eslint-disable-next-line @typescript-eslint/no-explicit-any\n        const edited: string | null | undefined = (root.root() as any).commitEdits?.();\n        if (typeof edited === 'string') return edited;\n      } catch {\n        // commitEdits not available \u2014 fall through to text substitution\n      }\n\n      // Fallback: apply replacements using byte offsets, processing from end to start\n      // so earlier replacements don't shift the offsets of later ones.\n      interface Edit { start: number; end: number; replacement: string }\n      const edits: Edit[] = [];\n      // eslint-disable-next-line @typescript-eslint/no-explicit-any\n      for (const node of nodes as any[]) {\n        const fixText = renderFix(rule.fix, node);\n        if (fixText === undefined) continue;\n        const range = node.range();\n        // Convert line/col to byte offset\n        const lines = fileContent.split('\\n');\n        let startOffset = 0;\n        for (let i = 0; i < range.start.line; i++) {\n          startOffset += (lines[i]?.length ?? 0) + 1; // +1 for \\n\n        }\n        startOffset += range.start.column;\n\n        let endOffset = 0;\n        for (let i = 0; i < range.end.line; i++) {\n          endOffset += (lines[i]?.length ?? 0) + 1;\n        }\n        endOffset += range.end.column;\n\n        edits.push({ start: startOffset, end: endOffset, replacement: fixText });\n      }\n\n      if (edits.length === 0) return null;\n\n      // Sort descending by start offset so we can splice without re-indexing\n      edits.sort((a, b) => b.start - a.start);\n\n      let result = fileContent;\n      for (const edit of edits) {\n        result = result.slice(0, edit.start) + edit.replacement + result.slice(edit.end);\n      }\n\n      return result !== fileContent ? result : null;\n    } catch (err) {\n      logWarn(`PatternRunner.applyFix: error applying fix for rule \"${rule.id}\" on \"${filePath}\": ${err instanceof Error ? err.message : String(err)}`);\n      return null;\n    }\n  }\n}\n\nfunction _buildContext(lines: string[], zeroBasedLine: number): string {\n  const contextLines: string[] = [];\n  if (zeroBasedLine > 0) contextLines.push(lines[zeroBasedLine - 1] ?? 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+  "sourcesContent": ["/**\n * KiroGraph PatternRunner \u2014 lazy-loads @ast-grep/napi and executes pattern rules.\n */\n\nimport { PatternRule, PatternMatch, SEVERITY_ORDER } from './types';\nimport { logWarn } from '../errors';\n\n// Languages the @ast-grep/napi binary bundles natively (its built-in Lang enum).\n// napi.Lang is an empty object at runtime (values are type-only), so we enumerate\n// these explicitly rather than reading from the export.\nconst NAPI_BUILTIN_LANGUAGES = new Set([\n  'html', 'javascript', 'jsx', 'typescript', 'tsx', 'css',\n]);\n\n// Module-level cache: undefined = not yet attempted, null = missing, module = loaded\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nlet _napi: any | null | undefined = undefined;\nlet _napiWarnLogged = false;\n// Runtime-detected set of languages the installed @ast-grep/napi actually supports,\n// derived from its Lang enum on first load. Null until napi has been loaded.\nlet _napiRuntimeLangs: Set<string> | null = null;\n\n// Optional language packages that extend napi beyond its built-in JS/TS/HTML/CSS set.\n// registerDynamicLanguage() loads a tree-sitter grammar .so for each entry.\n// Keys must match the language strings used in pattern rule files and the files table.\nconst DYNAMIC_LANG_PACKAGES: Record<string, string> = {\n  go:     '@ast-grep/lang-go',\n  python: '@ast-grep/lang-python',\n  java:   '@ast-grep/lang-java',\n  rust:   '@ast-grep/lang-rust',\n  c:      '@ast-grep/lang-c',\n  cpp:    '@ast-grep/lang-cpp',\n  cs:     '@ast-grep/lang-csharp',\n  kotlin: '@ast-grep/lang-kotlin',\n  swift:  '@ast-grep/lang-swift',\n  ruby:   '@ast-grep/lang-ruby',\n  php:    '@ast-grep/lang-php',\n  bash:   '@ast-grep/lang-bash',\n  scala:  '@ast-grep/lang-scala',\n  dart:   '@ast-grep/lang-dart',\n  lua:    '@ast-grep/lang-lua',\n  elixir: '@ast-grep/lang-elixir',\n  haskell:'@ast-grep/lang-haskell',\n};\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nasync function getNapi(): Promise<any | null> {\n  if (_napi !== undefined) return _napi;\n  try {\n    // Verify it can be resolved synchronously before async import\n    require.resolve('@ast-grep/napi');\n    // eslint-disable-next-line @typescript-eslint/no-require-imports\n    _napi = require('@ast-grep/napi');\n\n    // Register any installed dynamic language grammars. 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Pattern matching is disabled. 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package/dist/security/integrator.js

@@ -322,16 +322,16 @@ class DependencyGraphIntegrator {
     const ecosystemsWithLockFile = new Set(lockFiles.map((lf) => lf.ecosystem));
     for (const [ecosystem, depsMap] of depsByEcosystem) {
       if (!ecosystemsWithLockFile.has(ecosystem)) {
-        for (const [pkgName, nodeId] of depsMap) {
+        for (const [, nodeId] of depsMap) {
           rawDb.run(
             `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,
             [nodeId]
           );
           incompleteNodes.push(nodeId);
-          (0, import_errors.logWarn)(
-            `[sec:integrator] Transitive resolution incomplete for "${pkgName}" (${ecosystem}): no lock file found`
-          );
         }
+        (0, import_errors.logDebug)(
+          `[sec:integrator] No lock file parser for ${ecosystem} \u2014 transitive depth unavailable for ${depsMap.size} package(s). Direct vulnerability scanning is unaffected.`
+        );
       }
     }
     for (const lockFile of lockFiles) {
@@ -340,16 +340,16 @@ class DependencyGraphIntegrator {
       if (!ecosystemDeps) continue;
       if (transitives.length === 0 && ecosystemDeps.size > 0) {
         if (lockFile.ecosystem === "go" || lockFile.ecosystem === "python") {
-          for (const [pkgName, nodeId] of ecosystemDeps) {
+          for (const [, nodeId] of ecosystemDeps) {
             rawDb.run(
               `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,
               [nodeId]
             );
             incompleteNodes.push(nodeId);
-            (0, import_errors.logWarn)(
-              `[sec:integrator] Transitive resolution incomplete for "${pkgName}" (${lockFile.ecosystem}): dependency tree not resolvable from lock file`
-            );
           }
+          (0, import_errors.logDebug)(
+            `[sec:integrator] ${lockFile.ecosystem === "go" ? "go.sum" : "requirements.txt"} does not encode a dependency tree \u2014 transitive depth unavailable for ${ecosystemDeps.size} ${lockFile.ecosystem} package(s). Direct vulnerability scanning is unaffected.`
+          );
         }
         continue;
       }

package/dist/security/integrator.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/security/integrator.ts"],
-  "sourcesContent": ["/**\n * DependencyGraphIntegrator\n *\n * Links dependency nodes to code symbols via import and reference edges,\n * resolves transitive dependencies from lock files, and cleans up orphaned nodes.\n *\n * Integration flow:\n * 1. integrate() \u2014 Scan file nodes for import statements resolving to dependencies,\n *    create `imports` and `references` edges.\n * 2. resolveTransitives(maxDepth) \u2014 Parse lock files to discover transitive dependency\n *    relationships, create `depends_on` edges between Dependency_Nodes.\n * 3. cleanup() \u2014 Remove orphaned Dependency_Nodes no longer declared in any manifest.\n */\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport type { GraphDatabase } from '../db/database';\nimport type { Edge } from '../types';\nimport type { IntegrationResult, TransitiveResult, CleanupResult } from './types';\nimport { logWarn } from '../errors';\n\n// \u2500\u2500 Lock File Parsers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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 * Transitive dependency relationship: parent depends on child.\n */\ninterface TransitiveDep {\n  parent: string;\n  child: string;\n}\n\n/**\n * Parse package-lock.json (v2/v3) to extract transitive dependency relationships.\n * Returns pairs of (parent, child) where parent depends on child.\n */\nfunction parseNpmLockTransitives(lockPath: string): TransitiveDep[] {\n  const deps: TransitiveDep[] = [];\n  try {\n    const content = fs.readFileSync(lockPath, 'utf8');\n    const lockData = JSON.parse(content);\n\n    if (typeof lockData !== 'object' || lockData === null) return deps;\n\n    const packages = lockData.packages;\n    if (typeof packages !== 'object' || packages === null) {\n      // Try lockfileVersion 1 format\n      return parseNpmLockV1Transitives(lockData);\n    }\n\n    // lockfileVersion 2/3: packages field with nested node_modules paths\n    for (const [key, value] of Object.entries(packages as Record<string, unknown>)) {\n      if (key === '') continue; // skip root\n      if (typeof value !== 'object' || value === null) continue;\n      const pkg = value as Record<string, unknown>;\n\n      // Extract the package name from the key\n      const parentName = key.replace(/^.*node_modules\\//, '');\n      if (!parentName) continue;\n\n      // Extract this package's dependencies\n      const allDeps: Record<string, unknown> = {};\n      for (const field of ['dependencies', 'optionalDependencies', 'peerDependencies']) {\n        const fieldDeps = pkg[field];\n        if (typeof fieldDeps === 'object' && fieldDeps !== null) {\n          Object.assign(allDeps, fieldDeps);\n        }\n      }\n\n      for (const childName of Object.keys(allDeps)) {\n        deps.push({ parent: parentName, child: childName });\n      }\n    }\n  } catch {\n    // Lock file parse failure \u2014 return empty\n  }\n  return deps;\n}\n\n/**\n * Parse lockfileVersion 1 format (nested dependencies object).\n */\nfunction parseNpmLockV1Transitives(lockData: Record<string, unknown>): TransitiveDep[] {\n  const deps: TransitiveDep[] = [];\n  const topDeps = lockData.dependencies;\n  if (typeof topDeps !== 'object' || topDeps === null) return deps;\n\n  function recurse(parentDeps: Record<string, unknown>): void {\n    for (const [name, value] of Object.entries(parentDeps)) {\n      if (typeof value !== 'object' || value === null) continue;\n      const pkg = value as Record<string, unknown>;\n\n      // Check for requires (direct dependencies of this package)\n      const requires = pkg.requires;\n      if (typeof requires === 'object' && requires !== null) {\n        for (const childName of Object.keys(requires as Record<string, unknown>)) {\n          deps.push({ parent: name, child: childName });\n        }\n      }\n\n      // Recurse into nested dependencies\n      const nested = pkg.dependencies;\n      if (typeof nested === 'object' && nested !== null) {\n        recurse(nested as Record<string, unknown>);\n      }\n    }\n  }\n\n  recurse(topDeps as Record<string, unknown>);\n  return deps;\n}\n\n/**\n * Parse Cargo.lock to extract transitive dependency relationships.\n * Cargo.lock [[package]] blocks have a `dependencies` field listing direct deps.\n */\nfunction parseCargoLockTransitives(lockPath: string): TransitiveDep[] {\n  const deps: TransitiveDep[] = [];\n  try {\n    const content = fs.readFileSync(lockPath, 'utf8');\n    const lines = content.split('\\n');\n\n    let currentName: string | null = null;\n    let inDeps = false;\n\n    for (const line of lines) {\n      const trimmed = line.trim();\n\n      if (trimmed === '[[package]]') {\n        currentName = null;\n        inDeps = false;\n        continue;\n      }\n\n      if (currentName === null) {\n        const nameMatch = trimmed.match(/^name\\s*=\\s*\"([^\"]+)\"$/);\n        if (nameMatch) {\n          currentName = nameMatch[1];\n          continue;\n        }\n      }\n\n      if (currentName !== null && trimmed === 'dependencies = [') {\n        inDeps = true;\n        continue;\n      }\n\n      if (inDeps) {\n        if (trimmed === ']') {\n          inDeps = false;\n          continue;\n        }\n        // Lines like: \"serde_derive 1.0.193 (registry+...)\",\n        // or simply: \"serde_derive\",\n        const depMatch = trimmed.match(/^\\s*\"([^\"\\s]+)/);\n        if (depMatch && currentName) {\n          deps.push({ parent: currentName, child: depMatch[1] });\n        }\n      }\n    }\n  } catch {\n    // Lock file parse failure \u2014 return empty\n  }\n  return deps;\n}\n\n/**\n * Parse go.sum to extract module dependency relationships.\n * go.sum doesn't directly encode dependency trees, so we parse go.mod\n * for the require directives. For transitive resolution, we'd need\n * `go mod graph` output, but for the MVP we mark Go deps as incomplete\n * if no explicit dependency tree is available.\n *\n * Returns empty \u2014 Go transitive resolution requires `go mod graph` which\n * is not available at index time. Nodes will be marked incomplete.\n */\nfunction parseGoTransitives(_lockPath: string): TransitiveDep[] {\n  // Go modules don't have a lock file that encodes the dependency tree.\n  // go.sum only provides checksums. Full transitive resolution requires\n  // running `go mod graph` which is out of scope for static analysis.\n  return [];\n}\n\n/**\n * Parse pip's requirements files for transitive dependencies.\n * pip doesn't have a standard lock file with dependency trees.\n * Returns empty \u2014 nodes will be marked incomplete.\n */\nfunction parsePipTransitives(_lockPath: string): TransitiveDep[] {\n  return [];\n}\n\n// \u2500\u2500 Lock File Discovery \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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\ninterface LockFileInfo {\n  ecosystem: string;\n  lockPath: string;\n  parser: (lockPath: string) => TransitiveDep[];\n}\n\n/**\n * Discover lock files in the project root for each ecosystem.\n */\nfunction discoverLockFiles(projectRoot: string): LockFileInfo[] {\n  const lockFiles: LockFileInfo[] = [];\n\n  const candidates: Array<{ ecosystem: string; filename: string; parser: (p: string) => TransitiveDep[] }> = [\n    { ecosystem: 'npm', filename: 'package-lock.json', parser: parseNpmLockTransitives },\n    { ecosystem: 'npm', filename: 'yarn.lock', parser: parseNpmLockTransitives },\n    { ecosystem: 'cargo', filename: 'Cargo.lock', parser: parseCargoLockTransitives },\n    { ecosystem: 'go', filename: 'go.sum', parser: parseGoTransitives },\n    { ecosystem: 'python', filename: 'requirements.txt', parser: parsePipTransitives },\n  ];\n\n  for (const candidate of candidates) {\n    const lockPath = path.join(projectRoot, candidate.filename);\n    if (fs.existsSync(lockPath)) {\n      lockFiles.push({\n        ecosystem: candidate.ecosystem,\n        lockPath,\n        parser: candidate.parser,\n      });\n    }\n  }\n\n  return lockFiles;\n}\n\n// \u2500\u2500 DependencyGraphIntegrator Class \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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 class DependencyGraphIntegrator {\n  private readonly db: GraphDatabase;\n  private readonly projectRoot: string;\n\n  constructor(db: GraphDatabase, projectRoot: string) {\n    this.db = db;\n    this.projectRoot = projectRoot;\n  }\n\n  /**\n   * Create import/reference edges between code symbols and Dependency_Nodes.\n   *\n   * Per Requirement 2.1: creates `imports` edges from file nodes that contain\n   * import statements resolving to a dependency \u2192 the Dependency_Node.\n   *\n   * Per Requirement 2.2: creates `references` edges from code symbols that\n   * reference classes/functions from a dependency \u2192 the Dependency_Node.\n   */\n  async integrate(): Promise<IntegrationResult> {\n    let importsEdgesCreated = 0;\n    let referencesEdgesCreated = 0;\n\n    const rawDb = this.db.getRawDb();\n\n    // Get all dependency nodes with their package names and ecosystems\n    const depRows: Array<{ node_id: string; package_name: string; ecosystem: string }> =\n      rawDb.all('SELECT node_id, package_name, ecosystem FROM sec_dependencies');\n\n    if (depRows.length === 0) {\n      return { importsEdgesCreated, referencesEdgesCreated };\n    }\n\n    // Build a lookup map: package name \u2192 dependency node ID\n    const depByName = new Map<string, string>();\n    for (const row of depRows) {\n      depByName.set(row.package_name, row.node_id);\n    }\n\n    // \u2500\u2500 Step 1: Create `imports` edges (file \u2192 dependency) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    // Scan import nodes. The import node's `name` field contains the module\n    // specifier (e.g., 'express', '@nestjs/core', 'github.com/gin-gonic/gin').\n    // For each match, create an edge from the FILE node to the Dependency_Node.\n    const importNodes = this.db.getNodesByKind('import');\n\n    // Track (file, dep) pairs to avoid duplicate edges\n    const createdImportEdges = new Set<string>();\n\n    for (const importNode of importNodes) {\n      // Use the import node's `name` field which is the raw module specifier\n      const specifier = importNode.name;\n\n      const matchedDepId = this.matchImportToDependency(specifier, depByName);\n      if (!matchedDepId) continue;\n\n      // Find the file node for this import's file path\n      const fileNodeId = this.findFileNodeId(rawDb, importNode.filePath);\n      if (!fileNodeId) continue;\n\n      const edgeKey = `${fileNodeId}\u2192${matchedDepId}`;\n      if (createdImportEdges.has(edgeKey)) continue;\n\n      const edge: Edge = {\n        source: fileNodeId,\n        target: matchedDepId,\n        kind: 'imports',\n        line: importNode.startLine,\n        confidence: 'inferred',\n        confidenceScore: 0.9,\n      };\n      this.db.insertEdge(edge);\n      createdImportEdges.add(edgeKey);\n      importsEdgesCreated++;\n    }\n\n    // \u2500\u2500 Step 2: Create `references` edges (code symbol \u2192 dependency) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    // For each import node that matched a dependency, find code symbols in the\n    // same file that call or reference that import node. Those symbols effectively\n    // reference the dependency.\n    const codeKinds = new Set(['function', 'method', 'class', 'variable', 'constant', 'property']);\n    const createdRefEdges = new Set<string>();\n\n    for (const importNode of importNodes) {\n      const specifier = importNode.name;\n      const matchedDepId = this.matchImportToDependency(specifier, depByName);\n      if (!matchedDepId) continue;\n\n      // Get all nodes in the same file\n      const fileNodes = this.db.getNodesByFile(importNode.filePath);\n      const codeSymbols = fileNodes.filter(n => codeKinds.has(n.kind));\n      if (codeSymbols.length === 0) continue;\n\n      // Check edges from code symbols to this import node\n      const symbolIds = codeSymbols.map(n => n.id);\n      const edges = this.db.getEdgesForNodes(symbolIds);\n\n      for (const edge of edges) {\n        // A code symbol calls or references the import node \u2192 it references the dependency\n        if (\n          (edge.kind === 'calls' || edge.kind === 'references') &&\n          edge.target === importNode.id &&\n          symbolIds.includes(edge.source)\n        ) {\n          const refKey = `${edge.source}\u2192${matchedDepId}`;\n          if (createdRefEdges.has(refKey)) continue;\n\n          const refEdge: Edge = {\n            source: edge.source,\n            target: matchedDepId,\n            kind: 'references',\n            confidence: 'inferred',\n            confidenceScore: 0.8,\n          };\n          this.db.insertEdge(refEdge);\n          createdRefEdges.add(refKey);\n          referencesEdgesCreated++;\n        }\n      }\n    }\n\n    return { importsEdgesCreated, referencesEdgesCreated };\n  }\n\n  /**\n   * Find the file node ID for a given file path.\n   * File nodes have kind='file' and their file_path matches.\n   */\n  private findFileNodeId(rawDb: any, filePath: string): string | null {\n    const row = rawDb.get(\n      'SELECT id FROM nodes WHERE kind = ? AND file_path = ? LIMIT 1',\n      ['file', filePath],\n    );\n    return row ? row.id : null;\n  }\n\n  /**\n   * Match an import specifier to a dependency node ID.\n   *\n   * Handles:\n   * - Exact match: `express` \u2192 dep:npm:express\n   * - Scoped packages: `@scope/pkg` \u2192 dep:npm:@scope/pkg\n   * - Subpath imports: `express/Router` \u2192 dep:npm:express\n   * - Scoped subpath: `@angular/core/testing` \u2192 dep:npm:@angular/core\n   * - Go modules: `github.com/gin-gonic/gin` \u2192 dep:go:github.com/gin-gonic/gin\n   * - Go subpath: `github.com/gin-gonic/gin/internal` \u2192 dep:go:github.com/gin-gonic/gin\n   */\n  private matchImportToDependency(\n    specifier: string,\n    depByName: Map<string, string>,\n  ): string | null {\n    if (!specifier) return null;\n\n    // Skip relative imports\n    if (specifier.startsWith('.') || specifier.startsWith('/')) return null;\n\n    // Direct match\n    if (depByName.has(specifier)) {\n      return depByName.get(specifier)!;\n    }\n\n    // For scoped packages: @scope/name/subpath \u2192 @scope/name\n    if (specifier.startsWith('@')) {\n      const parts = specifier.split('/');\n      if (parts.length >= 2) {\n        const scopedName = `${parts[0]}/${parts[1]}`;\n        if (depByName.has(scopedName)) {\n          return depByName.get(scopedName)!;\n        }\n      }\n    }\n\n    // For unscoped packages: name/subpath \u2192 name\n    if (!specifier.startsWith('@')) {\n      const slashIdx = specifier.indexOf('/');\n      if (slashIdx > 0) {\n        const baseName = specifier.slice(0, slashIdx);\n        if (depByName.has(baseName)) {\n          return depByName.get(baseName)!;\n        }\n      }\n    }\n\n    // Go module path matching: try progressively shorter prefixes\n    // e.g. github.com/gin-gonic/gin/internal \u2192 github.com/gin-gonic/gin\n    if (specifier.includes('.') && specifier.includes('/')) {\n      const parts = specifier.split('/');\n      for (let i = parts.length - 1; i >= 2; i--) {\n        const prefix = parts.slice(0, i).join('/');\n        if (depByName.has(prefix)) {\n          return depByName.get(prefix)!;\n        }\n      }\n    }\n\n    return null;\n  }\n\n  /**\n   * Resolve transitive dependencies up to maxDepth levels.\n   *\n   * For each ecosystem with a lock file:\n   * 1. Parse the lock file to extract dependency relationships\n   * 2. Create `depends_on` edges between Dependency_Nodes\n   * 3. Traverse up to maxDepth levels of transitive depth\n   *\n   * If a lock file is missing for an ecosystem, mark all dependencies of that\n   * ecosystem with `transitive_status: 'incomplete'` and log a warning.\n   *\n   * @param maxDepth - Maximum levels of transitive depth to resolve (default: 10)\n   */\n  async resolveTransitives(maxDepth: number = 10): Promise<TransitiveResult> {\n    let dependsOnEdgesCreated = 0;\n    const incompleteNodes: string[] = [];\n    const rawDb = this.db.getRawDb();\n\n    // Get all dependency nodes grouped by ecosystem\n    const depRows: Array<{ node_id: string; package_name: string; ecosystem: string }> =\n      rawDb.all('SELECT node_id, package_name, ecosystem FROM sec_dependencies');\n\n    if (depRows.length === 0) {\n      return { dependsOnEdgesCreated, incompleteNodes };\n    }\n\n    // Group dependencies by ecosystem\n    const depsByEcosystem = new Map<string, Map<string, string>>();\n    for (const row of depRows) {\n      if (!depsByEcosystem.has(row.ecosystem)) {\n        depsByEcosystem.set(row.ecosystem, new Map());\n      }\n      depsByEcosystem.get(row.ecosystem)!.set(row.package_name, row.node_id);\n    }\n\n    // Discover available lock files\n    const lockFiles = discoverLockFiles(this.projectRoot);\n    const ecosystemsWithLockFile = new Set(lockFiles.map(lf => lf.ecosystem));\n\n    // Mark ecosystems without lock files as incomplete\n    for (const [ecosystem, depsMap] of depsByEcosystem) {\n      if (!ecosystemsWithLockFile.has(ecosystem)) {\n        // No lock file for this ecosystem \u2014 mark all deps as incomplete\n        for (const [pkgName, nodeId] of depsMap) {\n          rawDb.run(\n            `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,\n            [nodeId],\n          );\n          incompleteNodes.push(nodeId);\n          logWarn(\n            `[sec:integrator] Transitive resolution incomplete for \"${pkgName}\" (${ecosystem}): ` +\n            `no lock file found`,\n          );\n        }\n      }\n    }\n\n    // Parse each lock file and create depends_on edges\n    for (const lockFile of lockFiles) {\n      const transitives = lockFile.parser(lockFile.lockPath);\n      const ecosystemDeps = depsByEcosystem.get(lockFile.ecosystem);\n      if (!ecosystemDeps) continue;\n\n      if (transitives.length === 0 && ecosystemDeps.size > 0) {\n        // Lock file exists but yielded no transitive info (e.g., go.sum)\n        // Mark deps as incomplete if the parser couldn't extract tree info\n        if (lockFile.ecosystem === 'go' || lockFile.ecosystem === 'python') {\n          for (const [pkgName, nodeId] of ecosystemDeps) {\n            rawDb.run(\n              `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,\n              [nodeId],\n            );\n            incompleteNodes.push(nodeId);\n            logWarn(\n              `[sec:integrator] Transitive resolution incomplete for \"${pkgName}\" (${lockFile.ecosystem}): ` +\n              `dependency tree not resolvable from lock file`,\n            );\n          }\n        }\n        continue;\n      }\n\n      // Build adjacency list from transitive relationships\n      const adjacency = new Map<string, Set<string>>();\n      for (const { parent, child } of transitives) {\n        if (!adjacency.has(parent)) {\n          adjacency.set(parent, new Set());\n        }\n        adjacency.get(parent)!.add(child);\n      }\n\n      // BFS from each direct dependency up to maxDepth levels\n      // Create depends_on edges only between nodes that exist in our dep graph\n      const createdEdges = new Set<string>();\n\n      for (const [pkgName, nodeId] of ecosystemDeps) {\n        const visited = new Set<string>([pkgName]);\n        let frontier = [pkgName];\n        let depth = 0;\n\n        while (frontier.length > 0 && depth < maxDepth) {\n          const nextFrontier: string[] = [];\n          depth++;\n\n          for (const current of frontier) {\n            const children = adjacency.get(current);\n            if (!children) continue;\n\n            for (const child of children) {\n              if (visited.has(child)) continue;\n              visited.add(child);\n\n              // Create depends_on edge if the child is a known dependency node\n              const childNodeId = ecosystemDeps.get(child);\n              const parentNodeId = current === pkgName ? nodeId : ecosystemDeps.get(current);\n\n              if (parentNodeId && childNodeId) {\n                const edgeKey = `${parentNodeId}->${childNodeId}`;\n                if (!createdEdges.has(edgeKey)) {\n                  const edge: Edge = {\n                    source: parentNodeId,\n                    target: childNodeId,\n                    kind: 'depends_on',\n                    confidence: 'inferred',\n                    confidenceScore: 1.0,\n                  };\n                  this.db.insertEdge(edge);\n                  createdEdges.add(edgeKey);\n                  dependsOnEdgesCreated++;\n                }\n              }\n\n              nextFrontier.push(child);\n            }\n          }\n\n          frontier = nextFrontier;\n        }\n      }\n    }\n\n    return { dependsOnEdgesCreated, incompleteNodes };\n  }\n\n  /**\n   * Remove orphaned Dependency_Nodes and their edges.\n   *\n   * A Dependency_Node is orphaned if:\n   * 1. It has no `declared_in` edges (manifest no longer declares it), OR\n   * 2. None of its source manifests still exist on disk\n   *\n   * Also removes transitive Dependency_Nodes that are no longer reachable from\n   * any remaining direct dependency via `depends_on` edges.\n   *\n   * @param manifestExists - Optional function to check if a manifest path exists.\n   *   Defaults to fs.existsSync. Useful for testing.\n   */\n  async cleanup(manifestExists?: (absolutePath: string) => boolean): Promise<CleanupResult> {\n    let nodesRemoved = 0;\n    let edgesRemoved = 0;\n    const rawDb = this.db.getRawDb();\n    const checkExists = manifestExists ?? ((p: string) => fs.existsSync(p));\n\n    // Step 1: Find dependency nodes that are orphaned because they have no\n    // declared_in edges (manifest no longer declares them)\n    const orphanedByEdge: Array<{ node_id: string }> = rawDb.all(\n      `SELECT sd.node_id FROM sec_dependencies sd\n       WHERE NOT EXISTS (\n         SELECT 1 FROM edges e\n         WHERE e.source = sd.node_id AND e.kind = 'declared_in'\n       )`,\n    );\n\n    const orphanedNodeIds = new Set<string>(orphanedByEdge.map(r => r.node_id));\n\n    // Step 2: Also check if source manifests still exist on disk\n    const allDeps: Array<{ node_id: string; source_manifests: string }> = rawDb.all(\n      `SELECT node_id, source_manifests FROM sec_dependencies`,\n    );\n\n    for (const dep of allDeps) {\n      if (orphanedNodeIds.has(dep.node_id)) continue; // already marked\n\n      const sourceManifests: string[] = JSON.parse(dep.source_manifests);\n      const hasValidManifest = sourceManifests.some(manifest => {\n        const absolutePath = path.isAbsolute(manifest)\n          ? manifest\n          : path.join(this.projectRoot, manifest);\n        return checkExists(absolutePath);\n      });\n\n      if (!hasValidManifest) {\n        orphanedNodeIds.add(dep.node_id);\n      }\n    }\n\n    // Step 3: Find transitive Dependency_Nodes no longer reachable from any\n    // remaining direct dependency via `depends_on` edges\n    const remainingNodeIds = new Set<string>(\n      allDeps\n        .filter(d => !orphanedNodeIds.has(d.node_id))\n        .map(d => d.node_id),\n    );\n\n    // BFS from remaining nodes following `depends_on` edges to find all reachable transitives\n    const reachableFromDirect = new Set<string>(remainingNodeIds);\n    let frontier = [...remainingNodeIds];\n\n    while (frontier.length > 0) {\n      const placeholders = frontier.map(() => '?').join(',');\n      const nextRows: Array<{ target: string }> = rawDb.all(\n        `SELECT DISTINCT target FROM edges WHERE source IN (${placeholders}) AND kind = 'depends_on'`,\n        frontier,\n      );\n\n      frontier = [];\n      for (const row of nextRows) {\n        if (!reachableFromDirect.has(row.target)) {\n          reachableFromDirect.add(row.target);\n          frontier.push(row.target);\n        }\n      }\n    }\n\n    // Any dependency node that is NOT reachable from a remaining direct dependency is also orphaned\n    for (const dep of allDeps) {\n      if (!orphanedNodeIds.has(dep.node_id) && !reachableFromDirect.has(dep.node_id)) {\n        orphanedNodeIds.add(dep.node_id);\n      }\n    }\n\n    if (orphanedNodeIds.size === 0) {\n      return { nodesRemoved: 0, edgesRemoved: 0 };\n    }\n\n    // Step 4: Remove orphaned nodes and their edges\n    const orphanedIds = [...orphanedNodeIds];\n\n    for (const nodeId of orphanedIds) {\n      // Count edges being removed\n      const edgeCount = rawDb.get(\n        `SELECT COUNT(*) as c FROM edges\n         WHERE source = ? OR target = ?`,\n        [nodeId, nodeId],\n      );\n      edgesRemoved += edgeCount?.c ?? 0;\n\n      // Delete edges connected to this node\n      rawDb.run('DELETE FROM edges WHERE source = ? OR target = ?', [nodeId, nodeId]);\n\n      // Remove from sec_dependencies (explicit delete before nodes for clarity)\n      rawDb.run('DELETE FROM sec_dependencies WHERE node_id = ?', [nodeId]);\n\n      // Remove from nodes table\n      rawDb.run('DELETE FROM nodes WHERE id = ?', [nodeId]);\n\n      // Clean up FTS entries\n      rawDb.run('DELETE FROM nodes_fts WHERE id = ?', [nodeId]);\n\n      nodesRemoved++;\n    }\n\n    return { nodesRemoved, edgesRemoved };\n  }\n}\n"],
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Full transitive resolution requires\n  // running `go mod graph` which is out of scope for static analysis.\n  return [];\n}\n\n/**\n * Parse pip's requirements files for transitive dependencies.\n * pip doesn't have a standard lock file with dependency trees.\n * Returns empty \u2014 nodes will be marked incomplete.\n */\nfunction parsePipTransitives(_lockPath: string): TransitiveDep[] {\n  return [];\n}\n\n// \u2500\u2500 Lock File Discovery \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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\ninterface LockFileInfo {\n  ecosystem: string;\n  lockPath: string;\n  parser: (lockPath: string) => TransitiveDep[];\n}\n\n/**\n * Discover lock files in the project root for each ecosystem.\n */\nfunction discoverLockFiles(projectRoot: string): LockFileInfo[] {\n  const lockFiles: LockFileInfo[] = [];\n\n  const candidates: Array<{ ecosystem: string; filename: string; parser: (p: string) => TransitiveDep[] }> = [\n    { ecosystem: 'npm', filename: 'package-lock.json', parser: parseNpmLockTransitives },\n    { ecosystem: 'npm', filename: 'yarn.lock', parser: parseNpmLockTransitives },\n    { ecosystem: 'cargo', filename: 'Cargo.lock', parser: parseCargoLockTransitives },\n    { ecosystem: 'go', filename: 'go.sum', parser: parseGoTransitives },\n    { ecosystem: 'python', filename: 'requirements.txt', parser: parsePipTransitives },\n  ];\n\n  for (const candidate of candidates) {\n    const lockPath = path.join(projectRoot, candidate.filename);\n    if (fs.existsSync(lockPath)) {\n      lockFiles.push({\n        ecosystem: candidate.ecosystem,\n        lockPath,\n        parser: candidate.parser,\n      });\n    }\n  }\n\n  return lockFiles;\n}\n\n// \u2500\u2500 DependencyGraphIntegrator Class \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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 class DependencyGraphIntegrator {\n  private readonly db: GraphDatabase;\n  private readonly projectRoot: string;\n\n  constructor(db: GraphDatabase, projectRoot: string) {\n    this.db = db;\n    this.projectRoot = projectRoot;\n  }\n\n  /**\n   * Create import/reference edges between code symbols and Dependency_Nodes.\n   *\n   * Per Requirement 2.1: creates `imports` edges from file nodes that contain\n   * import statements resolving to a dependency \u2192 the Dependency_Node.\n   *\n   * Per Requirement 2.2: creates `references` edges from code symbols that\n   * reference classes/functions from a dependency \u2192 the Dependency_Node.\n   */\n  async integrate(): Promise<IntegrationResult> {\n    let importsEdgesCreated = 0;\n    let referencesEdgesCreated = 0;\n\n    const rawDb = this.db.getRawDb();\n\n    // Get all dependency nodes with their package names and ecosystems\n    const depRows: Array<{ node_id: string; package_name: string; ecosystem: string }> =\n      rawDb.all('SELECT node_id, package_name, ecosystem FROM sec_dependencies');\n\n    if (depRows.length === 0) {\n      return { importsEdgesCreated, referencesEdgesCreated };\n    }\n\n    // Build a lookup map: package name \u2192 dependency node ID\n    const depByName = new Map<string, string>();\n    for (const row of depRows) {\n      depByName.set(row.package_name, row.node_id);\n    }\n\n    // \u2500\u2500 Step 1: Create `imports` edges (file \u2192 dependency) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    // Scan import nodes. The import node's `name` field contains the module\n    // specifier (e.g., 'express', '@nestjs/core', 'github.com/gin-gonic/gin').\n    // For each match, create an edge from the FILE node to the Dependency_Node.\n    const importNodes = this.db.getNodesByKind('import');\n\n    // Track (file, dep) pairs to avoid duplicate edges\n    const createdImportEdges = new Set<string>();\n\n    for (const importNode of importNodes) {\n      // Use the import node's `name` field which is the raw module specifier\n      const specifier = importNode.name;\n\n      const matchedDepId = this.matchImportToDependency(specifier, depByName);\n      if (!matchedDepId) continue;\n\n      // Find the file node for this import's file path\n      const fileNodeId = this.findFileNodeId(rawDb, importNode.filePath);\n      if (!fileNodeId) continue;\n\n      const edgeKey = `${fileNodeId}\u2192${matchedDepId}`;\n      if (createdImportEdges.has(edgeKey)) continue;\n\n      const edge: Edge = {\n        source: fileNodeId,\n        target: matchedDepId,\n        kind: 'imports',\n        line: importNode.startLine,\n        confidence: 'inferred',\n        confidenceScore: 0.9,\n      };\n      this.db.insertEdge(edge);\n      createdImportEdges.add(edgeKey);\n      importsEdgesCreated++;\n    }\n\n    // \u2500\u2500 Step 2: Create `references` edges (code symbol \u2192 dependency) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    // For each import node that matched a dependency, find code symbols in the\n    // same file that call or reference that import node. 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AND file_path = ? LIMIT 1',\n      ['file', filePath],\n    );\n    return row ? row.id : null;\n  }\n\n  /**\n   * Match an import specifier to a dependency node ID.\n   *\n   * Handles:\n   * - Exact match: `express` \u2192 dep:npm:express\n   * - Scoped packages: `@scope/pkg` \u2192 dep:npm:@scope/pkg\n   * - Subpath imports: `express/Router` \u2192 dep:npm:express\n   * - Scoped subpath: `@angular/core/testing` \u2192 dep:npm:@angular/core\n   * - Go modules: `github.com/gin-gonic/gin` \u2192 dep:go:github.com/gin-gonic/gin\n   * - Go subpath: `github.com/gin-gonic/gin/internal` \u2192 dep:go:github.com/gin-gonic/gin\n   */\n  private matchImportToDependency(\n    specifier: string,\n    depByName: Map<string, string>,\n  ): string | null {\n    if (!specifier) return null;\n\n    // Skip relative imports\n    if (specifier.startsWith('.') || specifier.startsWith('/')) return null;\n\n    // Direct match\n    if (depByName.has(specifier)) {\n      return depByName.get(specifier)!;\n    }\n\n    // For scoped packages: @scope/name/subpath \u2192 @scope/name\n    if (specifier.startsWith('@')) {\n      const parts = specifier.split('/');\n      if (parts.length >= 2) {\n        const scopedName = `${parts[0]}/${parts[1]}`;\n        if (depByName.has(scopedName)) {\n          return depByName.get(scopedName)!;\n        }\n      }\n    }\n\n    // For unscoped packages: name/subpath \u2192 name\n    if (!specifier.startsWith('@')) {\n      const slashIdx = specifier.indexOf('/');\n      if (slashIdx > 0) {\n        const baseName = specifier.slice(0, slashIdx);\n        if (depByName.has(baseName)) {\n          return depByName.get(baseName)!;\n        }\n      }\n    }\n\n    // Go module path matching: try progressively shorter prefixes\n    // e.g. github.com/gin-gonic/gin/internal \u2192 github.com/gin-gonic/gin\n    if (specifier.includes('.') && specifier.includes('/')) {\n      const parts = specifier.split('/');\n      for (let i = parts.length - 1; i >= 2; i--) {\n        const prefix = parts.slice(0, i).join('/');\n        if (depByName.has(prefix)) {\n          return depByName.get(prefix)!;\n        }\n      }\n    }\n\n    return null;\n  }\n\n  /**\n   * Resolve transitive dependencies up to maxDepth levels.\n   *\n   * For each ecosystem with a lock file:\n   * 1. Parse the lock file to extract dependency relationships\n   * 2. Create `depends_on` edges between Dependency_Nodes\n   * 3. Traverse up to maxDepth levels of transitive depth\n   *\n   * If a lock file is missing for an ecosystem, mark all dependencies of that\n   * ecosystem with `transitive_status: 'incomplete'` and log a warning.\n   *\n   * @param maxDepth - Maximum levels of transitive depth to resolve (default: 10)\n   */\n  async resolveTransitives(maxDepth: number = 10): Promise<TransitiveResult> {\n    let dependsOnEdgesCreated = 0;\n    const incompleteNodes: string[] = [];\n    const rawDb = this.db.getRawDb();\n\n    // Get all dependency nodes grouped by ecosystem\n    const depRows: Array<{ node_id: string; package_name: string; ecosystem: string }> =\n      rawDb.all('SELECT node_id, package_name, ecosystem FROM sec_dependencies');\n\n    if (depRows.length === 0) {\n      return { dependsOnEdgesCreated, incompleteNodes };\n    }\n\n    // Group dependencies by ecosystem\n    const depsByEcosystem = new Map<string, Map<string, string>>();\n    for (const row of depRows) {\n      if (!depsByEcosystem.has(row.ecosystem)) {\n        depsByEcosystem.set(row.ecosystem, new Map());\n      }\n      depsByEcosystem.get(row.ecosystem)!.set(row.package_name, row.node_id);\n    }\n\n    // Discover available lock files\n    const lockFiles = discoverLockFiles(this.projectRoot);\n    const ecosystemsWithLockFile = new Set(lockFiles.map(lf => lf.ecosystem));\n\n    // Mark ecosystems without lock files as incomplete\n    for (const [ecosystem, depsMap] of depsByEcosystem) {\n      if (!ecosystemsWithLockFile.has(ecosystem)) {\n        // No lock file for this ecosystem \u2014 mark all deps as incomplete and log once per ecosystem.\n        for (const [, nodeId] of depsMap) {\n          rawDb.run(\n            `UPDATE sec_dependencies SET transitive_status = 'incomplete' WHERE node_id = ?`,\n            [nodeId],\n          );\n          incompleteNodes.push(nodeId);\n        }\n        logDebug(\n          `[sec:integrator] No lock file parser for ${ecosystem} \u2014 transitive depth unavailable for ` +\n          `${depsMap.size} package(s). Direct vulnerability scanning is unaffected.`,\n        );\n      }\n    }\n\n    // Parse each lock file and create depends_on edges\n    for (const lockFile of lockFiles) {\n      const transitives = lockFile.parser(lockFile.lockPath);\n      const ecosystemDeps = depsByEcosystem.get(lockFile.ecosystem);\n      if (!ecosystemDeps) continue;\n\n      if (transitives.length === 0 && ecosystemDeps.size > 0) {\n        // Lock file exists but yielded no transitive info (e.g., go.sum has only checksums,\n        // pip requirements.txt has no tree). 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Direct vulnerability scanning is unaffected.`,\n          );\n        }\n        continue;\n      }\n\n      // Build adjacency list from transitive relationships\n      const adjacency = new Map<string, Set<string>>();\n      for (const { parent, child } of transitives) {\n        if (!adjacency.has(parent)) {\n          adjacency.set(parent, new Set());\n        }\n        adjacency.get(parent)!.add(child);\n      }\n\n      // BFS from each direct dependency up to maxDepth levels\n      // Create depends_on edges only between nodes that exist in our dep graph\n      const createdEdges = new Set<string>();\n\n      for (const [pkgName, nodeId] of ecosystemDeps) {\n        const visited = new Set<string>([pkgName]);\n        let frontier = [pkgName];\n        let depth = 0;\n\n        while (frontier.length > 0 && depth < maxDepth) {\n          const nextFrontier: string[] = [];\n          depth++;\n\n          for (const current of frontier) {\n            const children = adjacency.get(current);\n            if (!children) continue;\n\n            for (const child of children) {\n              if (visited.has(child)) continue;\n              visited.add(child);\n\n              // Create depends_on edge if the child is a known dependency node\n              const childNodeId = ecosystemDeps.get(child);\n              const parentNodeId = current === pkgName ? nodeId : ecosystemDeps.get(current);\n\n              if (parentNodeId && childNodeId) {\n                const edgeKey = `${parentNodeId}->${childNodeId}`;\n                if (!createdEdges.has(edgeKey)) {\n                  const edge: Edge = {\n                    source: parentNodeId,\n                    target: childNodeId,\n                    kind: 'depends_on',\n                    confidence: 'inferred',\n                    confidenceScore: 1.0,\n                  };\n                  this.db.insertEdge(edge);\n                  createdEdges.add(edgeKey);\n                  dependsOnEdgesCreated++;\n                }\n              }\n\n              nextFrontier.push(child);\n            }\n          }\n\n          frontier = nextFrontier;\n        }\n      }\n    }\n\n    return { dependsOnEdgesCreated, incompleteNodes };\n  }\n\n  /**\n   * Remove orphaned Dependency_Nodes and their edges.\n   *\n   * A Dependency_Node is orphaned if:\n   * 1. 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OR target = ?`,\n        [nodeId, nodeId],\n      );\n      edgesRemoved += edgeCount?.c ?? 0;\n\n      // Delete edges connected to this node\n      rawDb.run('DELETE FROM edges WHERE source = ? OR target = ?', [nodeId, nodeId]);\n\n      // Remove from sec_dependencies (explicit delete before nodes for clarity)\n      rawDb.run('DELETE FROM sec_dependencies WHERE node_id = ?', [nodeId]);\n\n      // Remove from nodes table\n      rawDb.run('DELETE FROM nodes WHERE id = ?', [nodeId]);\n\n      // Clean up FTS entries\n      rawDb.run('DELETE FROM nodes_fts WHERE id = ?', [nodeId]);\n\n      nodesRemoved++;\n    }\n\n    return { nodesRemoved, edgesRemoved };\n  }\n}\n"],
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 }

package/dist/types.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../src/types.ts"],
-  "sourcesContent": ["/**\n * KiroGraph Type Definitions\n */\n\nexport type NodeKind =\n  | 'file' | 'module' | 'class' | 'struct' | 'interface' | 'trait' | 'protocol'\n  | 'function' | 'method' | 'property' | 'field' | 'variable' | 'constant'\n  | 'enum' | 'enum_member' | 'type_alias' | 'namespace' | 'parameter'\n  | 'import' | 'export' | 'route' | 'component'\n  | 'dependency' | 'vulnerability';\n\nexport type EdgeKind =\n  | 'contains' | 'calls' | 'imports' | 'exports' | 'extends' | 'implements'\n  | 'references' | 'type_of' | 'returns' | 'instantiates' | 'overrides' | 'decorates'\n  | 'has_vulnerability' | 'depends_on' | 'declared_in';\n\nexport type Language =\n  | 'typescript' | 'javascript' | 'tsx' | 'jsx' | 'python' | 'go' | 'rust'\n  | 'java' | 'c' | 'cpp' | 'csharp' | 'php' | 'ruby' | 'swift' | 'kotlin'\n  | 'dart' | 'svelte' | 'pascal' | 'liquid' | 'elixir'\n  | 'scala' | 'lua' | 'zig' | 'bash' | 'ocaml' | 'elm' | 'solidity' | 'vue' | 'objc'\n  | 'yaml' | 'hcl' | 'css' | 'scss' | 'html'\n  | 'jupyter'\n  | 'rescript' | 'sql' | 'r' | 'julia' | 'powershell' | 'perl' | 'astro' | 'gdscript' | 'nix' | 'verilog'\n  | 'unknown';\n\nexport interface Node {\n  id: string;\n  kind: NodeKind;\n  name: string;\n  qualifiedName: string;\n  filePath: string;\n  language: Language;\n  startLine: number;\n  endLine: number;\n  startColumn: number;\n  endColumn: number;\n  docstring?: string;\n  signature?: string;\n  visibility?: 'public' | 'private' | 'protected' | 'internal';\n  isExported?: boolean;\n  isAsync?: boolean;\n  isStatic?: boolean;\n  isAbstract?: boolean;\n  decorators?: string[];\n  typeParameters?: string[];\n  updatedAt: number;\n}\n\nexport interface Edge {\n  source: string;\n  target: string;\n  kind: EdgeKind;\n  metadata?: Record<string, unknown>;\n  line?: number;\n  column?: number;\n  confidence?: 'extracted' | 'inferred' | 'ambiguous';\n  confidenceScore?: number;\n}\n\nexport interface FileRecord {\n  path: string;\n  contentHash: string;\n  language: Language;\n  fileSize: number;\n  symbolCount: number;\n  indexedAt: number;\n}\n\nexport interface SearchResult {\n  node: Node;\n  score: number;\n  matchType: 'exact' | 'prefix' | 'fuzzy' | 'semantic';\n}\n\nexport interface SearchOptions {\n  kinds?: NodeKind[];\n  languages?: Language[];\n  limit?: number;\n  minScore?: number;\n}\n\nexport interface Subgraph {\n  nodes: Node[];\n  edges: Edge[];\n  entryPoints: string[];\n}\n\nexport interface NodeContext {\n  node: Node;\n  ancestors: Node[];\n  children: Node[];\n  callers: Node[];\n  callees: Node[];\n}\n\nexport interface NodeMetrics {\n  incomingEdgeCount: number;\n  outgoingEdgeCount: number;\n  callCount: number;\n  callerCount: number;\n  childCount: number;\n}\n\nexport interface GraphStats {\n  files: number;\n  nodes: number;\n  edges: number;\n  nodesByKind: Record<string, number>;\n  filesByLanguage: Record<string, number>;\n  dbSizeBytes: number;\n  embeddingCount: number;\n  embeddableNodeCount: number;\n  embeddingsEnabled: boolean;\n  embeddingModel: string;\n  useVecIndex: boolean;\n  semanticEngine: 'cosine' | 'sqlite-vec' | 'orama' | 'pglite' | 'lancedb' | 'qdrant' | 'typesense';\n  vecIndexCount: number;\n  engineFallback: string | null;\n  frameworks: string[];\n  architectureEnabled: boolean;\n  architectureStats?: { packages: number; layers: number; packageDeps: number };\n}\n\nexport interface TaskContext {\n  task: string;\n  entryPoints: Node[];\n  relatedNodes: Node[];\n  edges: Edge[];\n  codeSnippets: Map<string, string>;\n  summary: string;\n}\n\nexport interface IndexProgress {\n  phase: 'scanning' | 'parsing' | 'storing' | 'resolving' | 'detecting frameworks' | 'embeddings' | 'architecture' | 'security' | 'docs' | 'data' | 'patterns' | 'retrying';\n  current: number;\n  total: number;\n  currentFile?: string;\n  meta?: Record<string, unknown>;\n}\n\nexport interface IndexResult {\n  success: boolean;\n  filesIndexed: number;\n  nodesCreated: number;\n  edgesCreated: number;\n  errors: string[];\n  duration: number;\n}\n\nexport interface SyncResult {\n  added: string[];\n  modified: string[];\n  removed: string[];\n  nodesCreated: number;\n  nodesUpdated: number;\n  nodesRemoved: number;\n  edgesCreated: number;\n  edgesRemoved: number;\n  filesScanned: number;\n  errors: string[];\n  duration: number;\n}\n\n// \u2500\u2500 Error Classes (re-exported from src/errors.ts for backward compatibility) \u2500\u2500\n\nexport {\n  KiroGraphError,\n  FileError,\n  ParseError,\n  DatabaseError,\n  ConfigError,\n} from './errors';\n"],
-  "mappings": ";;;;;;;;;;;;;;;;;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAsKA,oBAMO;",
+  "sourcesContent": ["/**\n * KiroGraph Type Definitions\n */\n\nexport type NodeKind =\n  | 'file' | 'module' | 'class' | 'struct' | 'interface' | 'trait' | 'protocol'\n  | 'function' | 'method' | 'property' | 'field' | 'variable' | 'constant'\n  | 'enum' | 'enum_member' | 'type_alias' | 'namespace' | 'parameter'\n  | 'import' | 'export' | 'route' | 'component'\n  | 'dependency' | 'vulnerability';\n\nexport type EdgeKind =\n  | 'contains' | 'calls' | 'imports' | 'exports' | 'extends' | 'implements'\n  | 'references' | 'type_of' | 'returns' | 'instantiates' | 'overrides' | 'decorates'\n  | 'has_vulnerability' | 'depends_on' | 'declared_in';\n\nexport type Language =\n  | 'typescript' | 'javascript' | 'tsx' | 'jsx' | 'python' | 'go' | 'rust'\n  | 'java' | 'c' | 'cpp' | 'csharp' | 'php' | 'ruby' | 'swift' | 'kotlin'\n  | 'dart' | 'svelte' | 'pascal' | 'liquid' | 'elixir'\n  | 'scala' | 'lua' | 'zig' | 'bash' | 'ocaml' | 'elm' | 'solidity' | 'vue' | 'objc'\n  | 'yaml' | 'hcl' | 'css' | 'scss' | 'html'\n  | 'jupyter'\n  | 'rescript' | 'sql' | 'r' | 'julia' | 'powershell' | 'perl' | 'astro' | 'gdscript' | 'nix' | 'verilog'\n  | 'haskell'\n  | 'unknown';\n\nexport interface Node {\n  id: string;\n  kind: NodeKind;\n  name: string;\n  qualifiedName: string;\n  filePath: string;\n  language: Language;\n  startLine: number;\n  endLine: number;\n  startColumn: number;\n  endColumn: number;\n  docstring?: string;\n  signature?: string;\n  visibility?: 'public' | 'private' | 'protected' | 'internal';\n  isExported?: boolean;\n  isAsync?: boolean;\n  isStatic?: boolean;\n  isAbstract?: boolean;\n  decorators?: string[];\n  typeParameters?: string[];\n  updatedAt: number;\n}\n\nexport interface Edge {\n  source: string;\n  target: string;\n  kind: EdgeKind;\n  metadata?: Record<string, unknown>;\n  line?: number;\n  column?: number;\n  confidence?: 'extracted' | 'inferred' | 'ambiguous';\n  confidenceScore?: number;\n}\n\nexport interface FileRecord {\n  path: string;\n  contentHash: string;\n  language: Language;\n  fileSize: number;\n  symbolCount: number;\n  indexedAt: number;\n}\n\nexport interface SearchResult {\n  node: Node;\n  score: number;\n  matchType: 'exact' | 'prefix' | 'fuzzy' | 'semantic';\n}\n\nexport interface SearchOptions {\n  kinds?: NodeKind[];\n  languages?: Language[];\n  limit?: number;\n  minScore?: number;\n}\n\nexport interface Subgraph {\n  nodes: Node[];\n  edges: Edge[];\n  entryPoints: string[];\n}\n\nexport interface NodeContext {\n  node: Node;\n  ancestors: Node[];\n  children: Node[];\n  callers: Node[];\n  callees: Node[];\n}\n\nexport interface NodeMetrics {\n  incomingEdgeCount: number;\n  outgoingEdgeCount: number;\n  callCount: number;\n  callerCount: number;\n  childCount: number;\n}\n\nexport interface GraphStats {\n  files: number;\n  nodes: number;\n  edges: number;\n  nodesByKind: Record<string, number>;\n  filesByLanguage: Record<string, number>;\n  dbSizeBytes: number;\n  embeddingCount: number;\n  embeddableNodeCount: number;\n  embeddingsEnabled: boolean;\n  embeddingModel: string;\n  useVecIndex: boolean;\n  semanticEngine: 'cosine' | 'sqlite-vec' | 'orama' | 'pglite' | 'lancedb' | 'qdrant' | 'typesense';\n  vecIndexCount: number;\n  engineFallback: string | null;\n  frameworks: string[];\n  architectureEnabled: boolean;\n  architectureStats?: { packages: number; layers: number; packageDeps: number };\n}\n\nexport interface TaskContext {\n  task: string;\n  entryPoints: Node[];\n  relatedNodes: Node[];\n  edges: Edge[];\n  codeSnippets: Map<string, string>;\n  summary: string;\n}\n\nexport interface IndexProgress {\n  phase: 'scanning' | 'parsing' | 'storing' | 'resolving' | 'detecting frameworks' | 'embeddings' | 'architecture' | 'security' | 'docs' | 'data' | 'patterns' | 'retrying';\n  current: number;\n  total: number;\n  currentFile?: string;\n  meta?: Record<string, unknown>;\n}\n\nexport interface IndexResult {\n  success: boolean;\n  filesIndexed: number;\n  nodesCreated: number;\n  edgesCreated: number;\n  errors: string[];\n  duration: number;\n}\n\nexport interface SyncResult {\n  added: string[];\n  modified: string[];\n  removed: string[];\n  nodesCreated: number;\n  nodesUpdated: number;\n  nodesRemoved: number;\n  edgesCreated: number;\n  edgesRemoved: number;\n  filesScanned: number;\n  errors: string[];\n  duration: number;\n}\n\n// \u2500\u2500 Error Classes (re-exported from src/errors.ts for backward compatibility) \u2500\u2500\n\nexport {\n  KiroGraphError,\n  FileError,\n  ParseError,\n  DatabaseError,\n  ConfigError,\n} from './errors';\n"],
+  "mappings": ";;;;;;;;;;;;;;;;;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAuKA,oBAMO;",
   "names": []
 }

package/dist/vectors/turboquant-index.js

@@ -0,0 +1,261 @@
+"use strict";
+var __create = Object.create;
+var __defProp = Object.defineProperty;
+var __getOwnPropDesc = Object.getOwnPropertyDescriptor;
+var __getOwnPropNames = Object.getOwnPropertyNames;
+var __getProtoOf = Object.getPrototypeOf;
+var __hasOwnProp = Object.prototype.hasOwnProperty;
+var __export = (target, all) => {
+  for (var name in all)
+    __defProp(target, name, { get: all[name], enumerable: true });
+};
+var __copyProps = (to, from, except, desc) => {
+  if (from && typeof from === "object" || typeof from === "function") {
+    for (let key of __getOwnPropNames(from))
+      if (!__hasOwnProp.call(to, key) && key !== except)
+        __defProp(to, key, { get: () => from[key], enumerable: !(desc = __getOwnPropDesc(from, key)) || desc.enumerable });
+  }
+  return to;
+};
+var __toESM = (mod, isNodeMode, target) => (target = mod != null ? __create(__getProtoOf(mod)) : {}, __copyProps(
+  // If the importer is in node compatibility mode or this is not an ESM
+  // file that has been converted to a CommonJS file using a Babel-
+  // compatible transform (i.e. "__esModule" has not been set), then set
+  // "default" to the CommonJS "module.exports" for node compatibility.
+  isNodeMode || !mod || !mod.__esModule ? __defProp(target, "default", { value: mod, enumerable: true }) : target,
+  mod
+));
+var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: true }), mod);
+var turboquant_index_exports = {};
+__export(turboquant_index_exports, {
+  TurboQuantIndex: () => TurboQuantIndex,
+  readTurboQuantStats: () => readTurboQuantStats,
+  writeTurboQuantStats: () => writeTurboQuantStats
+});
+module.exports = __toCommonJS(turboquant_index_exports);
+var path = __toESM(require("path"));
+var fs = __toESM(require("fs"));
+var import_errors = require("../errors");
+const STATS_FILE = "turboquant-stats.json";
+function readTurboQuantStats(kirographDir) {
+  try {
+    const p = path.join(kirographDir, STATS_FILE);
+    if (!fs.existsSync(p)) return null;
+    return JSON.parse(fs.readFileSync(p, "utf8"));
+  } catch {
+    return null;
+  }
+}
+function writeTurboQuantStats(kirographDir, patch) {
+  const p = path.join(kirographDir, STATS_FILE);
+  const tmp = p + ".tmp";
+  try {
+    const existing = readTurboQuantStats(kirographDir) ?? {
+      count: 0,
+      dim: 768,
+      bits: 3,
+      compressionRatio: 1,
+      actualBytes: 0,
+      rawBytes: 0,
+      savedBytes: 0,
+      memEnabled: false,
+      memCount: 0,
+      memActualBytes: 0,
+      memRawBytes: 0,
+      docsEnabled: false,
+      docsCount: 0,
+      docsActualBytes: 0,
+      docsRawBytes: 0,
+      updatedAt: 0
+    };
+    const updated = { ...existing, ...patch, updatedAt: Math.floor(Date.now() / 1e3) };
+    fs.writeFileSync(tmp, JSON.stringify(updated, null, 2));
+    fs.renameSync(tmp, p);
+  } catch (err) {
+    (0, import_errors.logWarn)("TurboQuantIndex: failed to write stats file", { error: String(err) });
+    try {
+      fs.unlinkSync(tmp);
+    } catch {
+    }
+  }
+}
+class TurboQuantIndex {
+  constructor(kirographDir, binName, dim, bits = 3) {
+    this.kirographDir = kirographDir;
+    this.binName = binName;
+    this.dim = dim;
+    this.bits = bits;
+    this.index = null;
+    this._available = false;
+  }
+  isAvailable() {
+    return this._available;
+  }
+  /**
+   * Load turboquant-js and restore index from disk if the .bin file exists.
+   * Silent no-op when the optional dependency is missing.
+   */
+  async initialize() {
+    if (this._available) return;
+    let TQModule;
+    try {
+      TQModule = require("turboquant-js");
+    } catch {
+      (0, import_errors.logDebug)("TurboQuantIndex: turboquant-js not installed \u2014 turboquant engine unavailable");
+      return;
+    }
+    const VectorIndex = TQModule?.VectorIndex ?? TQModule?.default?.VectorIndex ?? (typeof TQModule === "function" ? TQModule : null);
+    if (!VectorIndex || typeof VectorIndex !== "function") {
+      (0, import_errors.logWarn)("TurboQuantIndex: unrecognised turboquant-js module shape \u2014 turboquant engine unavailable");
+      return;
+    }
+    const binPath = path.join(this.kirographDir, this.binName);
+    try {
+      if (fs.existsSync(binPath) && typeof VectorIndex.fromBuffer === "function") {
+        const nodeBuf = fs.readFileSync(binPath);
+        const ab = nodeBuf.buffer.slice(nodeBuf.byteOffset, nodeBuf.byteOffset + nodeBuf.byteLength);
+        this.index = VectorIndex.fromBuffer(ab, { dimension: this.dim, bits: this.bits });
+        (0, import_errors.logDebug)("TurboQuantIndex: restored from disk", { binPath });
+      } else {
+        this.index = new VectorIndex({ dimension: this.dim, bits: this.bits });
+        (0, import_errors.logDebug)("TurboQuantIndex: new index", { dim: this.dim, bits: this.bits });
+      }
+      this._available = true;
+    } catch (err) {
+      (0, import_errors.logError)("TurboQuantIndex: initialization failed", { error: String(err) });
+      this._available = false;
+      this.index = null;
+    }
+  }
+  /** Add or update an embedding (turboquant-js compresses at index time). */
+  upsert(id, vec) {
+    if (!this._available || !this.index) return;
+    try {
+      this.index.add(id, vec);
+    } catch (err) {
+      (0, import_errors.logWarn)("TurboQuantIndex: upsert failed", { id, error: String(err) });
+    }
+  }
+  /** Remove an entry from the index (permanent via turboquant-js remove()). */
+  delete(id) {
+    if (!this._available || !this.index) return;
+    try {
+      this.index.remove(id);
+    } catch (err) {
+      (0, import_errors.logWarn)("TurboQuantIndex: delete failed", { id, error: String(err) });
+    }
+  }
+  /** ANN search: returns IDs sorted by descending similarity. */
+  search(queryVec, topN = 10) {
+    return this.searchWithScores(queryVec, topN).map((r) => r.id);
+  }
+  /**
+   * ANN search: returns [{id, score}] sorted by descending similarity.
+   * Used by MemoryVectorManager and DocsVectorManager to preserve scores for
+   * hybrid merge.
+   */
+  searchWithScores(queryVec, topN = 10) {
+    if (!this._available || !this.index) return [];
+    try {
+      const raw = this.index.search(queryVec, topN);
+      return this._normaliseSearchResults(raw).slice(0, topN);
+    } catch (err) {
+      (0, import_errors.logWarn)("TurboQuantIndex: search failed", { error: String(err) });
+      return [];
+    }
+  }
+  /**
+   * Persist the compressed index to disk atomically.
+   * Called once at the end of `kirograph index` — not on every upsert.
+   */
+  async save() {
+    if (!this._available || !this.index) return;
+    if (typeof this.index.toBuffer !== "function") {
+      (0, import_errors.logDebug)("TurboQuantIndex: toBuffer() not available \u2014 index not persisted");
+      return;
+    }
+    const binPath = path.join(this.kirographDir, this.binName);
+    const tmp = binPath + ".tmp";
+    try {
+      const raw = this.index.toBuffer();
+      const buf = raw instanceof ArrayBuffer ? Buffer.from(raw) : raw;
+      fs.writeFileSync(tmp, buf);
+      fs.renameSync(tmp, binPath);
+      (0, import_errors.logDebug)("TurboQuantIndex: saved", { binPath, bytes: buf.length });
+    } catch (err) {
+      (0, import_errors.logWarn)("TurboQuantIndex: save failed", { error: String(err) });
+      try {
+        fs.unlinkSync(tmp);
+      } catch {
+      }
+    }
+  }
+  /**
+   * Memory usage stats from the compressed index.
+   * Falls back to a formula-based estimate when memoryUsage is unavailable.
+   */
+  memoryStats() {
+    if (this._available && this.index?.memoryUsage) {
+      return this.index.memoryUsage;
+    }
+    const n = this.count();
+    const rawBytes = n * this.dim * 4;
+    const actualBytes = Math.ceil(n * this.dim * this.bits / 8);
+    return {
+      totalBits: actualBytes * 8,
+      bitsPerVector: this.bits * this.dim,
+      compressionRatio: actualBytes > 0 ? rawBytes / actualBytes : 1,
+      actualBytes
+    };
+  }
+  count() {
+    if (!this._available || !this.index) return 0;
+    try {
+      if (this.index.idToIndex instanceof Map) return this.index.idToIndex.size;
+      if (typeof this.index.size === "number") return this.index.size;
+    } catch {
+    }
+    return 0;
+  }
+  /** All IDs currently in the index. */
+  getEmbeddedIds() {
+    if (!this._available || !this.index) return [];
+    try {
+      if (this.index.idToIndex instanceof Map) {
+        return [...this.index.idToIndex.keys()];
+      }
+    } catch {
+    }
+    return [];
+  }
+  close() {
+    this.index = null;
+    this._available = false;
+  }
+  // ── Private ────────────────────────────────────────────────────────────────
+  _normaliseSearchResults(raw) {
+    if (!Array.isArray(raw)) return [];
+    return raw.map((item, rank) => {
+      if (item && typeof item === "object" && !Array.isArray(item)) {
+        const obj = item;
+        const id = obj["id"] ?? obj["key"] ?? "";
+        const score = obj["score"] ?? obj["similarity"] ?? obj["distance"] ?? 1 - rank / raw.length;
+        return { id, score: typeof score === "number" ? score : 1 - rank / raw.length };
+      }
+      if (Array.isArray(item) && item.length >= 2) {
+        return { id: String(item[0]), score: typeof item[1] === "number" ? item[1] : 1 - rank / raw.length };
+      }
+      if (typeof item === "string") {
+        return { id: item, score: 1 - rank / raw.length };
+      }
+      return null;
+    }).filter((r) => r !== null && r.id.length > 0);
+  }
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  TurboQuantIndex,
+  readTurboQuantStats,
+  writeTurboQuantStats
+});
+//# sourceMappingURL=turboquant-index.js.map