kirograph 0.23.0 → 0.26.0

package/dist/db/database.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/db/database.ts"],
-  "sourcesContent": ["/**\n * KiroGraph Database Layer\n * Wraps node-sqlite3-wasm for portability (no native bindings needed).\n */\n\nimport * as path from 'path';\nimport * as fs from 'fs';\nimport type { Node, Edge, FileRecord, NodeKind, Language, GraphStats, NodeContext, NodeMetrics, SearchOptions } from '../types';\nimport type { ArchPackage, ArchLayer, ArchPackageDep, ArchLayerDep, ArchCoupling } from '../architecture/types';\n\n// eslint-disable-next-line @typescript-eslint/no-require-imports\nconst { Database } = require('node-sqlite3-wasm');\n\nconst CURRENT_SCHEMA_VERSION = 1;\n\nexport class GraphDatabase {\n  private db: any;\n  private projectRoot: string;\n\n  constructor(projectRoot: string) {\n    this.projectRoot = projectRoot;\n    const dbDir = path.join(projectRoot, '.kirograph');\n    fs.mkdirSync(dbDir, { recursive: true });\n    const dbPath = path.join(dbDir, 'kirograph.db');\n\n    // \u2500\u2500 Pre-flight lock 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\n    // node-sqlite3-wasm calls process.abort() when the DB is locked, producing\n    // a cryptic \"Aborted()\" with no context. Detect the lock file early and\n    // throw a clean error instead so the global handler can surface it clearly.\n    const lockPath = path.join(dbDir, 'kirograph.db.lock');\n    if (fs.existsSync(lockPath)) {\n      throw new Error(\n        `Database is locked by another process (${lockPath} exists).\\n` +\n        `Run: kirograph unlock\\n` +\n        `Or delete the lock manually: ${lockPath}`\n      );\n    }\n\n    this.db = new Database(dbPath);\n    this.db.exec(`\n      PRAGMA journal_mode=WAL;\n      PRAGMA foreign_keys=ON;\n      PRAGMA busy_timeout=120000;\n      PRAGMA synchronous=NORMAL;\n      PRAGMA cache_size=-64000;\n      PRAGMA temp_store=MEMORY;\n      PRAGMA mmap_size=268435456;\n    `);\n    this.applySchema();\n  }\n\n  private applySchema(): void {\n    const schemaPath = path.join(__dirname, '../db/schema.sql');\n    const sql = fs.readFileSync(schemaPath, 'utf8');\n    this.db.exec(sql);\n    this.runMigrations();\n  }\n\n  /**\n   * Apply memory schema tables. Called when enableMemory is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyMemorySchema(): void {\n    const schemaPath = path.join(__dirname, '../db/memory-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n  }\n\n  /**\n   * Apply docs schema tables. Called when enableDocs is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyDocsSchema(): void {\n    const schemaPath = path.join(__dirname, '../db/docs-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n  }\n\n  /**\n   * Apply data schema tables. Called when enableData is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyDataSchema(): void {\n    const schemaPath = path.join(__dirname, '../db/data-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n    // Migrate existing DBs: add columns introduced after initial release.\n    const tryAlter = (stmt: string) => { try { this.db.run(stmt); } catch { /* already exists */ } };\n    tryAlter('ALTER TABLE data_datasets ADD COLUMN metadata_json TEXT');\n  }\n\n  /**\n   * Apply patterns schema tables. Called when enablePatterns is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyPatternsSchema(): void {\n    const schemaPath = path.join(__dirname, '../db/patterns-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n    // Migrate existing DBs: add new columns introduced after initial release.\n    const tryAlter = (stmt: string) => { try { this.db.run(stmt); } catch { /* already exists */ } };\n    tryAlter('ALTER TABLE pattern_matches ADD COLUMN symbol_node_id TEXT');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_pm_symbol ON pattern_matches(symbol_node_id)');\n  }\n\n  /**\n   * Apply security schema tables. Called when enableSecurity is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applySecuritySchema(): void {\n    const schemaPath = path.join(__dirname, '../db/security-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n    // Migrate existing DBs: add new columns introduced after initial release.\n    const tryAlter = (stmt: string) => { try { this.db.run(stmt); } catch { /* already exists */ } };\n    tryAlter('ALTER TABLE sec_dependencies ADD COLUMN license TEXT');\n    tryAlter('ALTER TABLE sec_dependencies ADD COLUMN latest_version TEXT');\n    tryAlter('ALTER TABLE sec_dependencies ADD COLUMN latest_published INTEGER');\n    tryAlter('ALTER TABLE sec_dependencies ADD COLUMN staleness_score REAL');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN epss_score REAL');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN epss_percentile REAL');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN epss_fetched_at INTEGER');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_sec_deps_license ON sec_dependencies(license)');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_sec_deps_staleness ON sec_dependencies(staleness_score)');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_sec_vulns_epss ON sec_vulnerabilities(epss_score)');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN risk_score REAL');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_sec_vulns_risk ON sec_vulnerabilities(risk_score)');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN first_detected_at INTEGER');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN fix_available_since INTEGER');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN suppressed_at INTEGER');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN remediated_at INTEGER');\n  }\n\n  /**\n   * Get the raw database handle (for MemoryDatabase).\n   */\n  getRawDb(): any {\n    return this.db;\n  }\n\n  private runMigrations(): void {\n    // Record initial schema version if not present\n    const versionRow = this.db.get('SELECT version FROM schema_versions ORDER BY version DESC LIMIT 1');\n    const currentVersion = versionRow ? versionRow.version : 0;\n\n    if (currentVersion < CURRENT_SCHEMA_VERSION) {\n      // Migration 1: schema.sql now includes all columns \u2014 nothing extra needed.\n      // The schema CREATE IF NOT EXISTS statements handle initial setup.\n      this.db.run('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)',\n        [CURRENT_SCHEMA_VERSION, Date.now()]);\n    }\n\n    // Add attempted_strategies column to unresolved_refs if not present.\n    // SQLite throws if the column already exists, so we catch that error.\n    try {\n      this.db.run('ALTER TABLE unresolved_refs ADD COLUMN attempted_strategies TEXT');\n    } catch {\n      // Column already exists \u2014 nothing to do.\n    }\n\n    // Add confidence columns to edges if not present.\n    try {\n      this.db.run(\"ALTER TABLE edges ADD COLUMN confidence TEXT NOT NULL DEFAULT 'extracted'\");\n    } catch {\n      // Column already exists \u2014 nothing to do.\n    }\n    try {\n      this.db.run('ALTER TABLE edges ADD COLUMN confidence_score REAL NOT NULL DEFAULT 1.0');\n    } catch {\n      // Column already exists \u2014 nothing to do.\n    }\n  }\n\n  // \u2500\u2500 Files \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  upsertFile(record: FileRecord): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO files (path, content_hash, language, file_size, symbol_count, indexed_at)\n       VALUES (?, ?, ?, ?, ?, ?)`,\n      [record.path, record.contentHash, record.language, record.fileSize, record.symbolCount, record.indexedAt]\n    );\n  }\n\n  getFile(filePath: string): FileRecord | null {\n    const row = this.db.get('SELECT * FROM files WHERE path = ?', [filePath]);\n    return row ? this.rowToFile(row) : null;\n  }\n\n  getAllFiles(): FileRecord[] {\n    return this.db.all('SELECT * FROM files').map(this.rowToFile);\n  }\n\n  deleteFile(filePath: string): void {\n    // Cascade deletes nodes (and their edges via FK)\n    this.db.run('DELETE FROM nodes WHERE file_path = ?', [filePath]);\n    this.db.run('DELETE FROM files WHERE path = ?', [filePath]);\n  }\n\n  private rowToFile(row: any): FileRecord {\n    return {\n      path: row.path,\n      contentHash: row.content_hash,\n      language: row.language as Language,\n      fileSize: row.file_size,\n      symbolCount: row.symbol_count,\n      indexedAt: row.indexed_at,\n    };\n  }\n\n  // \u2500\u2500 Nodes \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  upsertNode(node: Node): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO nodes\n        (id, kind, name, qualified_name, file_path, language,\n         start_line, end_line, start_column, end_column,\n         docstring, signature, visibility,\n         is_exported, is_async, is_static, is_abstract,\n         decorators, type_parameters, updated_at)\n       VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)`,\n      [\n        node.id, node.kind, node.name, node.qualifiedName, node.filePath, node.language,\n        node.startLine, node.endLine, node.startColumn, node.endColumn,\n        node.docstring ?? null, node.signature ?? null, node.visibility ?? null,\n        node.isExported ? 1 : 0, node.isAsync ? 1 : 0,\n        node.isStatic ? 1 : 0, node.isAbstract ? 1 : 0,\n        node.decorators ? JSON.stringify(node.decorators) : null,\n        node.typeParameters ? JSON.stringify(node.typeParameters) : null,\n        node.updatedAt,\n      ]\n    );\n    // Keep FTS in sync\n    this.db.run(\n      `INSERT OR REPLACE INTO nodes_fts (id, name, qualified_name, docstring, signature)\n       VALUES (?, ?, ?, ?, ?)`,\n      [node.id, node.name, node.qualifiedName, node.docstring ?? '', node.signature ?? '']\n    );\n  }\n\n  getNode(id: string): Node | null {\n    const row = this.db.get('SELECT * FROM nodes WHERE id = ?', [id]);\n    return row ? this.rowToNode(row) : null;\n  }\n\n  getNodesByFile(filePath: string): Node[] {\n    return this.db.all('SELECT * FROM nodes WHERE file_path = ?', [filePath]).map(this.rowToNode);\n  }\n\n  getNodesByKind(kind: Node['kind']): Node[] {\n    return this.db.all('SELECT * FROM nodes WHERE kind = ?', [kind]).map(this.rowToNode);\n  }\n\n  findNodesByExactName(name: string, kinds?: NodeKind[], limit = 20): Node[] {\n    if (kinds && kinds.length > 0) {\n      const placeholders = kinds.map(() => '?').join(',');\n      return this.db.all(\n        `SELECT * FROM nodes WHERE name = ? AND kind IN (${placeholders}) LIMIT ?`,\n        [name, ...kinds, limit]\n      ).map(this.rowToNode);\n    }\n    return this.db.all(\n      'SELECT * FROM nodes WHERE name = ? LIMIT ?',\n      [name, limit]\n    ).map(this.rowToNode);\n  }\n\n  searchNodes(query: string, opts: SearchOptions = {}): Node[] {\n    const { kinds, languages, limit = 20 } = opts;\n    // Sanitize for FTS5: strip special chars and append wildcard.\n    // Both the MATCH value and LIMIT are inlined (not bound via ?) because\n    // node-sqlite3-wasm passes bound parameters through to FTS5's own query\n    // parser before SQLite substitutes them, causing \"syntax error near ?\".\n    const safe = query\n      .replace(/\\b(AND|OR|NOT)\\b/g, ' ')       // FTS5 boolean operators\n      .replace(/['\"*()?\\-+^~:{}\\\\\\.\\/,]/g, ' ')  // FTS5 special chars (incl. / and ,)\n      .replace(/\\s+/g, ' ')\n      .trim();\n    if (!safe) return [];\n\n    const ftsQuery = safe + '*';\n    const safeLimit = Math.max(1, Math.floor(Number(limit)));\n\n    const conditions: string[] = [];\n    const params: any[] = [];\n\n    if (kinds && kinds.length > 0) {\n      conditions.push(`kind IN (${kinds.map(() => '?').join(',')})`);\n      params.push(...kinds);\n    }\n    if (languages && languages.length > 0) {\n      conditions.push(`language IN (${languages.map(() => '?').join(',')})`);\n      params.push(...languages);\n    }\n\n    const where = conditions.length > 0 ? `AND ${conditions.join(' AND ')}` : '';\n\n    return this.db.all(\n      `SELECT * FROM nodes\n       WHERE id IN (SELECT rowid FROM nodes_fts WHERE nodes_fts MATCH '${ftsQuery}')\n       ${where}\n       LIMIT ${safeLimit}`,\n      params\n    ).map(this.rowToNode);\n  }\n\n  searchNodesByName(name: string, opts: SearchOptions = {}): Node[] {\n    const { kinds, languages, limit = 20 } = opts;\n    const pattern = `%${name}%`;\n    const conditions: string[] = ['name LIKE ?'];\n    const params: any[] = [pattern];\n\n    if (kinds && kinds.length > 0) {\n      conditions.push(`kind IN (${kinds.map(() => '?').join(',')})`);\n      params.push(...kinds);\n    }\n    if (languages && languages.length > 0) {\n      conditions.push(`language IN (${languages.map(() => '?').join(',')})`);\n      params.push(...languages);\n    }\n    params.push(limit);\n\n    return this.db.all(\n      `SELECT * FROM nodes WHERE ${conditions.join(' AND ')} LIMIT ?`,\n      params\n    ).map(this.rowToNode);\n  }\n\n  deleteNodesByFile(filePath: string): void {\n    const ids = this.db.all('SELECT id FROM nodes WHERE file_path = ?', [filePath]).map((r: any) => r.id);\n    if (ids.length === 0) return;\n    const placeholders = ids.map(() => '?').join(',');\n    this.db.run(`DELETE FROM edges WHERE source IN (${placeholders}) OR target IN (${placeholders})`, [...ids, ...ids]);\n    this.db.run(`DELETE FROM nodes_fts WHERE id IN (${placeholders})`, ids);\n    this.db.run(`DELETE FROM nodes WHERE file_path = ?`, [filePath]);\n  }\n\n  private rowToNode(row: any): Node {\n    return {\n      id: row.id,\n      kind: row.kind as NodeKind,\n      name: row.name,\n      qualifiedName: row.qualified_name,\n      filePath: row.file_path,\n      language: row.language as Language,\n      startLine: row.start_line,\n      endLine: row.end_line,\n      startColumn: row.start_column,\n      endColumn: row.end_column,\n      docstring: row.docstring ?? undefined,\n      signature: row.signature ?? undefined,\n      visibility: row.visibility ?? undefined,\n      isExported: row.is_exported === 1,\n      isAsync: row.is_async === 1,\n      isStatic: row.is_static === 1,\n      isAbstract: row.is_abstract === 1,\n      decorators: row.decorators ? JSON.parse(row.decorators) : undefined,\n      typeParameters: row.type_parameters ? JSON.parse(row.type_parameters) : undefined,\n      updatedAt: row.updated_at,\n    };\n  }\n\n  // \u2500\u2500 Edges \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  insertEdge(edge: Edge): void {\n    this.db.run(\n      `INSERT OR IGNORE INTO edges (source, target, kind, metadata, line, column, confidence, confidence_score)\n       VALUES (?, ?, ?, ?, ?, ?, ?, ?)`,\n      [edge.source, edge.target, edge.kind, edge.metadata ? JSON.stringify(edge.metadata) : null, edge.line ?? null, edge.column ?? null, edge.confidence ?? 'extracted', edge.confidenceScore ?? 1.0]\n    );\n  }\n\n  getCallers(nodeId: string, limit = 30): Node[] {\n    return this.db.all(\n      `SELECT n.* FROM nodes n\n       JOIN edges e ON e.source = n.id\n       WHERE e.target = ? AND e.kind = 'calls'\n       LIMIT ?`,\n      [nodeId, limit]\n    ).map(this.rowToNode);\n  }\n\n  getCallees(nodeId: string, limit = 30): Node[] {\n    return this.db.all(\n      `SELECT n.* FROM nodes n\n       JOIN edges e ON e.target = n.id\n       WHERE e.source = ? AND e.kind = 'calls'\n       LIMIT ?`,\n      [nodeId, limit]\n    ).map(this.rowToNode);\n  }\n\n  getImpactRadius(nodeId: string, depth = 2): Node[] {\n    // BFS over 'calls' and 'imports' edges (dependents)\n    const visited = new Set<string>([nodeId]);\n    let frontier = [nodeId];\n    for (let d = 0; d < depth; d++) {\n      if (frontier.length === 0) break;\n      const placeholders = frontier.map(() => '?').join(',');\n      const rows = this.db.all(\n        `SELECT DISTINCT source FROM edges WHERE target IN (${placeholders}) AND kind IN ('calls','imports')`,\n        frontier\n      );\n      frontier = [];\n      for (const row of rows) {\n        if (!visited.has(row.source)) {\n          visited.add(row.source);\n          frontier.push(row.source);\n        }\n      }\n    }\n    visited.delete(nodeId);\n    if (visited.size === 0) return [];\n    const ids = [...visited];\n    const placeholders = ids.map(() => '?').join(',');\n    return this.db.all(`SELECT * FROM nodes WHERE id IN (${placeholders})`, ids).map(this.rowToNode);\n  }\n\n  getEdgesForNodes(nodeIds: string[]): Edge[] {\n    if (nodeIds.length === 0) return [];\n    const placeholders = nodeIds.map(() => '?').join(',');\n    return this.db.all(\n      `SELECT * FROM edges WHERE source IN (${placeholders}) OR target IN (${placeholders})`,\n      [...nodeIds, ...nodeIds]\n    ).map((row: any) => ({\n      source: row.source,\n      target: row.target,\n      kind: row.kind,\n      metadata: row.metadata ? JSON.parse(row.metadata) : undefined,\n      line: row.line ?? undefined,\n      column: row.column ?? undefined,\n    }));\n  }\n\n  /**\n   * Find files that import (depend on) the given file path.\n   * Used for affected-test traversal.\n   */\n  getDependentFiles(filePath: string): string[] {\n    // Find nodes in the target file\n    const targetNodes = this.db.all('SELECT id FROM nodes WHERE file_path = ?', [filePath]);\n    if (targetNodes.length === 0) return [];\n    const ids = targetNodes.map((r: any) => r.id);\n    const placeholders = ids.map(() => '?').join(',');\n    // Find source nodes that call/import these target nodes\n    const rows = this.db.all(\n      `SELECT DISTINCT n.file_path FROM nodes n\n       JOIN edges e ON e.source = n.id\n       WHERE e.target IN (${placeholders}) AND e.kind IN ('calls','imports')\n       AND n.file_path != ?`,\n      [...ids, filePath]\n    );\n    return rows.map((r: any) => r.file_path);\n  }\n\n  // \u2500\u2500 Unresolved References \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  insertUnresolvedRef(sourceId: string, refName: string, refKind: string, filePath: string, line?: number, column?: number): void {\n    this.db.run(\n      `INSERT INTO unresolved_refs (source_id, ref_name, ref_kind, file_path, line, column)\n       VALUES (?, ?, ?, ?, ?, ?)`,\n      [sourceId, refName, refKind, filePath, line ?? null, column ?? null]\n    );\n  }\n\n  deleteUnresolvedRefsByFile(filePath: string): void {\n    this.db.run('DELETE FROM unresolved_refs WHERE file_path = ?', [filePath]);\n  }\n\n  /**\n   * Resolve pending references:\n   * - refKind='function': 3-strategy name matching \u2192 'calls' edge\n   * - refKind='import': path-based resolution \u2192 'imports' edge\n   *\n   * Returns the number of edges successfully created.\n   */\n  resolveUnresolvedRefs(): number {\n    const refs = this.db.all('SELECT * FROM unresolved_refs');\n    let resolved = 0;\n\n    for (const ref of refs) {\n      const { id: refId, source_id: sourceId, ref_name: refName, ref_kind: refKind, file_path: filePath, line, column } = ref;\n\n      if (refKind === 'function') {\n        // Strategy 1: exact name match\n        let target = this.db.get('SELECT id FROM nodes WHERE name = ? LIMIT 1', [refName]);\n        let confidence: 'extracted' | 'inferred' | 'ambiguous' = 'inferred';\n        let confidenceScore = 1.0;\n\n        // Strategy 2: qualified name suffix\n        if (!target) {\n          target = this.db.get(\n            `SELECT id FROM nodes WHERE qualified_name LIKE ? LIMIT 1`,\n            [`%::${refName}`]\n          );\n        }\n\n        // Strategy 3: case-insensitive\n        if (!target) {\n          target = this.db.get(\n            'SELECT id FROM nodes WHERE lower(name) = lower(?) LIMIT 1',\n            [refName]\n          );\n          // Case-insensitive match is less certain\n          if (target) confidenceScore = 0.8;\n        }\n\n        // Check if there are multiple candidates (ambiguous)\n        if (target) {\n          const candidateCount = this.db.get('SELECT COUNT(*) as cnt FROM nodes WHERE name = ?', [refName]);\n          if (candidateCount && candidateCount.cnt > 1) {\n            confidence = 'ambiguous';\n            confidenceScore = 1.0 / candidateCount.cnt;\n          }\n        }\n\n        if (target) {\n          this.insertEdge({ source: sourceId, target: target.id, kind: 'calls', line: line ?? undefined, column: column ?? undefined, confidence, confidenceScore });\n          this.db.run('DELETE FROM unresolved_refs WHERE id = ?', [refId]);\n          resolved++;\n        }\n      } else if (refKind === 'import') {\n        // Resolve import path to an indexed file\n        const targetFileNode = this.resolveImportPath(refName, filePath);\n        if (targetFileNode) {\n          this.insertEdge({ source: sourceId, target: targetFileNode, kind: 'imports', line: line ?? undefined, column: column ?? undefined, confidence: 'inferred', confidenceScore: 1.0 });\n          this.db.run('DELETE FROM unresolved_refs WHERE id = ?', [refId]);\n          resolved++;\n        }\n      }\n    }\n\n    return resolved;\n  }\n\n  /** @deprecated Use resolveUnresolvedRefs() */\n  resolveCallEdges(): number {\n    return this.resolveUnresolvedRefs();\n  }\n\n  /**\n   * Resolve a module import path to the ID of the first node in the target file.\n   * Returns null if no indexed file matches.\n   */\n  private resolveImportPath(importPath: string, sourceFilePath: string): string | null {\n    // Only resolve relative imports\n    if (!importPath.startsWith('.')) return null;\n\n    const sourceDir = sourceFilePath.replace(/[^/]+$/, '');\n    // Normalize the relative path\n    const segments = (sourceDir + importPath).split('/');\n    const normalized: string[] = [];\n    for (const seg of segments) {\n      if (seg === '..') normalized.pop();\n      else if (seg !== '.') normalized.push(seg);\n    }\n    const basePath = normalized.join('/');\n\n    // Try exact match, then with common extensions\n    const candidates = [\n      basePath,\n      basePath + '.ts',\n      basePath + '.tsx',\n      basePath + '.js',\n      basePath + '.jsx',\n      basePath + '/index.ts',\n      basePath + '/index.tsx',\n      basePath + '/index.js',\n    ];\n\n    for (const candidate of candidates) {\n      const row = this.db.get('SELECT id FROM nodes WHERE file_path = ? LIMIT 1', [candidate]);\n      if (row) return row.id;\n    }\n\n    return null;\n  }\n\n  // \u2500\u2500 Node Context & Metrics \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  getNodeContext(nodeId: string): NodeContext | null {\n    const node = this.getNode(nodeId);\n    if (!node) return null;\n\n    const ancestors = this.db.all(\n      `SELECT n.* FROM nodes n\n       JOIN edges e ON e.target = n.id\n       WHERE e.source = ? AND e.kind = 'contains'`,\n      [nodeId]\n    ).map(this.rowToNode);\n\n    const children = this.db.all(\n      `SELECT n.* FROM nodes n\n       JOIN edges e ON e.source = n.id\n       WHERE e.target = n.id AND e.source = ? AND e.kind = 'contains'`,\n      [nodeId]\n    ).map(this.rowToNode);\n\n    const callers = this.getCallers(nodeId, 20);\n    const callees = this.getCallees(nodeId, 20);\n\n    return { node, ancestors, children, callers, callees };\n  }\n\n  getNodeMetrics(nodeId: string): NodeMetrics {\n    const incomingEdgeCount = (this.db.get('SELECT COUNT(*) as c FROM edges WHERE target = ?', [nodeId])?.c ?? 0);\n    const outgoingEdgeCount = (this.db.get('SELECT COUNT(*) as c FROM edges WHERE source = ?', [nodeId])?.c ?? 0);\n    const callCount = (this.db.get(`SELECT COUNT(*) as c FROM edges WHERE source = ? AND kind = 'calls'`, [nodeId])?.c ?? 0);\n    const callerCount = (this.db.get(`SELECT COUNT(*) as c FROM edges WHERE target = ? AND kind = 'calls'`, [nodeId])?.c ?? 0);\n    const childCount = (this.db.get(`SELECT COUNT(*) as c FROM edges WHERE source = ? AND kind = 'contains'`, [nodeId])?.c ?? 0);\n    return { incomingEdgeCount, outgoingEdgeCount, callCount, callerCount, childCount };\n  }\n\n  // \u2500\u2500 Graph Analysis \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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   * Find symbols with no incoming edges (potential dead code).\n   * Excludes exported symbols since they may be consumed externally.\n   */\n  findDeadCode(limit = 50): Node[] {\n    return this.db.all(\n      `SELECT * FROM nodes\n       WHERE kind IN ('function','method','class')\n         AND is_exported = 0\n         AND id NOT IN (SELECT DISTINCT target FROM edges)\n       LIMIT ?`,\n      [limit]\n    ).map(this.rowToNode);\n  }\n\n  /**\n   * Find circular import dependencies using DFS over import edges.\n   * Returns arrays of file paths forming cycles.\n   */\n  findCircularDependencies(): string[][] {\n    // Build adjacency map: file \u2192 imported files\n    const rows = this.db.all(\n      `SELECT DISTINCT n1.file_path as src, n2.file_path as dst\n       FROM edges e\n       JOIN nodes n1 ON n1.id = e.source\n       JOIN nodes n2 ON n2.id = e.target\n       WHERE e.kind = 'imports' AND n1.file_path != n2.file_path`\n    );\n\n    const adj = new Map<string, Set<string>>();\n    for (const row of rows) {\n      if (!adj.has(row.src)) adj.set(row.src, new Set());\n      adj.get(row.src)!.add(row.dst);\n    }\n\n    const cycles: string[][] = [];\n    const visited = new Set<string>();\n    const pathSet = new Set<string>();\n    const pathArr: string[] = [];\n\n    function dfs(node: string): void {\n      if (pathSet.has(node)) {\n        const cycleStart = pathArr.indexOf(node);\n        cycles.push(pathArr.slice(cycleStart).concat(node));\n        return;\n      }\n      if (visited.has(node)) return;\n      visited.add(node);\n      pathSet.add(node);\n      pathArr.push(node);\n      for (const neighbor of adj.get(node) ?? []) {\n        dfs(neighbor);\n      }\n      pathArr.pop();\n      pathSet.delete(node);\n    }\n\n    for (const node of adj.keys()) {\n      if (!visited.has(node)) dfs(node);\n    }\n\n    return cycles;\n  }\n\n  /**\n   * Find the shortest path between two nodes via directed BFS (outgoing edges only).\n   */\n  findPath(fromId: string, toId: string, maxDepth = 10): Node[] {\n    if (fromId === toId) {\n      const node = this.getNode(fromId);\n      return node ? [node] : [];\n    }\n\n    const prev = new Map<string, string>();\n    const queue: string[] = [fromId];\n    const visited = new Set<string>([fromId]);\n    let depth = 0;\n\n    outer: while (queue.length > 0 && depth < maxDepth) {\n      const levelSize = queue.length;\n      depth++;\n      for (let i = 0; i < levelSize; i++) {\n        const current = queue.shift()!;\n        // Directed: only follow outgoing edges\n        const rows = this.db.all(\n          `SELECT DISTINCT target as next FROM edges WHERE source = ?`,\n          [current]\n        );\n        for (const row of rows) {\n          if (!visited.has(row.next)) {\n            visited.add(row.next);\n            prev.set(row.next, current);\n            if (row.next === toId) break outer;\n            queue.push(row.next);\n          }\n        }\n      }\n    }\n\n    if (!prev.has(toId)) return [];\n\n    // Reconstruct path\n    const pathIds: string[] = [];\n    let cur: string | undefined = toId;\n    while (cur !== undefined) {\n      pathIds.unshift(cur);\n      cur = prev.get(cur);\n    }\n\n    const result: Node[] = [];\n    for (const id of pathIds) {\n      const node = this.getNode(id);\n      if (node) result.push(node);\n    }\n    return result;\n  }\n\n  /**\n   * Traverse type hierarchy via 'extends' and 'implements' edges.\n   * direction 'up' = base types, 'down' = derived types, 'both' = all.\n   */\n  getTypeHierarchy(nodeId: string, direction: 'up' | 'down' | 'both' = 'both'): Node[] {\n    const visited = new Set<string>([nodeId]);\n    const frontier = [nodeId];\n    const result: Node[] = [];\n\n    while (frontier.length > 0) {\n      const current = frontier.shift()!;\n      let rows: any[] = [];\n\n      if (direction === 'up' || direction === 'both') {\n        // current extends/implements something \u2192 go up\n        const up = this.db.all(\n          `SELECT target as id FROM edges WHERE source = ? AND kind IN ('extends','implements')`,\n          [current]\n        );\n        rows = rows.concat(up);\n      }\n      if (direction === 'down' || direction === 'both') {\n        // something extends/implements current \u2192 go down\n        const down = this.db.all(\n          `SELECT source as id FROM edges WHERE target = ? AND kind IN ('extends','implements')`,\n          [current]\n        );\n        rows = rows.concat(down);\n      }\n\n      for (const row of rows) {\n        if (!visited.has(row.id)) {\n          visited.add(row.id);\n          frontier.push(row.id);\n          const node = this.getNode(row.id);\n          if (node) result.push(node);\n        }\n      }\n    }\n\n    return result;\n  }\n\n  // \u2500\u2500 Stats \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  getEmbeddingCount(): number {\n    try {\n      const row = this.db.get('SELECT COUNT(*) as c FROM vectors');\n      return row ? row.c : 0;\n    } catch {\n      return 0;\n    }\n  }\n\n  storeEmbedding(nodeId: string, embedding: Float32Array, model: string): void {\n    const buf = Buffer.from(embedding.buffer);\n    this.db.run(\n      `INSERT OR REPLACE INTO vectors (node_id, embedding, model, created_at) VALUES (?, ?, ?, ?)`,\n      [nodeId, buf, model, Date.now()]\n    );\n  }\n\n  getEmbeddedNodeIds(): string[] {\n    return this.db.all('SELECT node_id FROM vectors').map((r: any) => r.node_id);\n  }\n\n  getAllEmbeddings(): Array<{ nodeId: string; embedding: Float32Array }> {\n    const rows = this.db.all('SELECT node_id, embedding FROM vectors');\n    return rows.map((r: any) => ({\n      nodeId: r.node_id as string,\n      embedding: new Float32Array(\n        (r.embedding as Buffer).buffer,\n        (r.embedding as Buffer).byteOffset,\n        (r.embedding as Buffer).byteLength / 4\n      ),\n    }));\n  }\n\n  getAllNodes(): import('../types').Node[] {\n    return this.db.all('SELECT * FROM nodes').map(this.rowToNode);\n  }\n\n  /**\n   * Returns embeddable nodes in pages for memory-efficient streaming.\n   * `kinds` filters by node kind (e.g. ['function','method','class']).\n   * Returns an empty array when offset >= total count.\n   */\n  getEmbeddableNodesPaged(kinds: string[], limit: number, offset: number): import('../types').Node[] {\n    if (kinds.length === 0) return [];\n    const placeholders = kinds.map(() => '?').join(',');\n    return this.db.all(\n      `SELECT * FROM nodes WHERE kind IN (${placeholders}) LIMIT ? OFFSET ?`,\n      [...kinds, limit, offset]\n    ).map(this.rowToNode);\n  }\n\n  /** Count of nodes whose kind is in the provided list. */\n  countEmbeddableNodes(kinds: string[]): number {\n    if (kinds.length === 0) return 0;\n    const placeholders = kinds.map(() => '?').join(',');\n    const row = this.db.get(`SELECT COUNT(*) as c FROM nodes WHERE kind IN (${placeholders})`, kinds);\n    return row?.c ?? 0;\n  }\n\n  getAllEdges(): Edge[] {\n    return this.db.all('SELECT source, target, kind FROM edges').map((row: any) => ({\n      source: row.source,\n      target: row.target,\n      kind: row.kind,\n    }));\n  }\n\n  /**\n   * Find the top-N most-connected nodes by total edge degree (in + out).\n   * Excludes 'contains' edges (structural nesting, not semantic connections).\n   */\n  findHotspots(limit = 20): Array<Node & { degree: number; inDegree: number; outDegree: number }> {\n    const rows = this.db.all(\n      `SELECT n.*,\n         (SELECT COUNT(*) FROM edges WHERE target = n.id AND kind != 'contains') AS in_degree,\n         (SELECT COUNT(*) FROM edges WHERE source = n.id AND kind != 'contains') AS out_degree,\n         (SELECT COUNT(*) FROM edges WHERE (source = n.id OR target = n.id) AND kind != 'contains') AS degree\n       FROM nodes n\n       ORDER BY degree DESC\n       LIMIT ?`,\n      [limit]\n    );\n    return rows.map((row: any) => ({\n      ...this.rowToNode(row),\n      degree: row.degree as number,\n      inDegree: row.in_degree as number,\n      outDegree: row.out_degree as number,\n    }));\n  }\n\n  /**\n   * Find surprising cross-file connections: direct edges between nodes in\n   * structurally distant files. Scored by path distance \u00D7 edge-kind weight.\n   */\n  findSurprisingConnections(limit = 20): Array<{ source: Node; target: Node; kind: string; score: number }> {\n    const KIND_WEIGHT: Record<string, number> = {\n      calls: 1.0, references: 0.8, type_of: 0.7, returns: 0.6,\n      decorates: 0.6, extends: 0.5, implements: 0.5,\n    };\n\n    const rows: Array<{ source: string; target: string; kind: string; source_file: string; target_file: string }> =\n      this.db.all(\n        `SELECT e.source, e.target, e.kind,\n                ns.file_path AS source_file, nt.file_path AS target_file\n         FROM edges e\n         JOIN nodes ns ON ns.id = e.source\n         JOIN nodes nt ON nt.id = e.target\n         WHERE ns.file_path != nt.file_path\n           AND e.kind NOT IN ('contains', 'import', 'imports')\n         LIMIT 5000`\n      );\n\n    // Score: path distance \u00D7 kind weight\n    const scored = rows.map(row => {\n      const srcDirs = row.source_file.split('/').slice(0, -1);\n      const tgtDirs = row.target_file.split('/').slice(0, -1);\n      let common = 0;\n      for (let i = 0; i < Math.min(srcDirs.length, tgtDirs.length); i++) {\n        if (srcDirs[i] === tgtDirs[i]) common++;\n        else break;\n      }\n      const maxDirs = Math.max(srcDirs.length, tgtDirs.length, 1);\n      const pathSimilarity = common / maxDirs;\n      const kindWeight = KIND_WEIGHT[row.kind] ?? 0.4;\n      return { ...row, score: (1 - pathSimilarity) * kindWeight };\n    });\n\n    // Sort desc, deduplicate by source+target+kind\n    scored.sort((a, b) => b.score - a.score);\n    const seen = new Set<string>();\n    const top: typeof scored = [];\n    for (const row of scored) {\n      const key = `${row.source}|${row.target}|${row.kind}`;\n      if (!seen.has(key)) {\n        seen.add(key);\n        top.push(row);\n        if (top.length >= limit) break;\n      }\n    }\n\n    const result: Array<{ source: Node; target: Node; kind: string; score: number }> = [];\n    for (const row of top) {\n      const src = this.getNode(row.source);\n      const tgt = this.getNode(row.target);\n      if (src && tgt) result.push({ source: src, target: tgt, kind: row.kind, score: row.score });\n    }\n    return result;\n  }\n\n  getStats(): GraphStats {\n    const files = this.db.get('SELECT COUNT(*) as c FROM files').c;\n    const nodes = this.db.get('SELECT COUNT(*) as c FROM nodes').c;\n    const edges = this.db.get('SELECT COUNT(*) as c FROM edges').c;\n    const kindRows = this.db.all('SELECT kind, COUNT(*) as c FROM nodes GROUP BY kind');\n    const nodesByKind: Record<string, number> = {};\n    for (const row of kindRows) nodesByKind[row.kind] = row.c;\n    const langRows = this.db.all('SELECT language, COUNT(*) as c FROM files GROUP BY language');\n    const filesByLanguage: Record<string, number> = {};\n    for (const row of langRows) filesByLanguage[row.language] = row.c;\n    const dbPath = path.join(this.projectRoot, '.kirograph', 'kirograph.db');\n    let dbSizeBytes = 0;\n    try { dbSizeBytes = fs.statSync(dbPath).size; } catch { /* ignore */ }\n    const embeddingCount = this.getEmbeddingCount();\n    return { files, nodes, edges, nodesByKind, filesByLanguage, dbSizeBytes, embeddingCount, embeddingsEnabled: false, embeddingModel: '', useVecIndex: false, semanticEngine: 'cosine' as const, vecIndexCount: 0, engineFallback: null, embeddableNodeCount: 0, frameworks: [], architectureEnabled: false };\n  }\n\n  // \u2500\u2500 Architecture \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  clearArchitecture(): void {\n    this.db.run('DELETE FROM arch_coupling');\n    this.db.run('DELETE FROM arch_layer_deps');\n    this.db.run('DELETE FROM arch_package_deps');\n    this.db.run('DELETE FROM arch_file_layers');\n    this.db.run('DELETE FROM arch_file_packages');\n    this.db.run('DELETE FROM arch_layers');\n    this.db.run('DELETE FROM arch_packages');\n  }\n\n  upsertArchPackage(pkg: ArchPackage): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_packages\n        (id, name, path, source, language, manifest_path, version, external_deps, metadata, updated_at)\n       VALUES (?,?,?,?,?,?,?,?,?,?)`,\n      [\n        pkg.id, pkg.name, pkg.path, pkg.source,\n        pkg.language ?? null, pkg.manifestPath ?? null, pkg.version ?? null,\n        pkg.externalDeps ? JSON.stringify(pkg.externalDeps) : null,\n        pkg.metadata ? JSON.stringify(pkg.metadata) : null,\n        pkg.updatedAt,\n      ]\n    );\n  }\n\n  upsertArchLayer(layer: ArchLayer): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_layers (id, name, source, patterns, metadata, updated_at)\n       VALUES (?,?,?,?,?,?)`,\n      [\n        layer.id, layer.name, layer.source,\n        JSON.stringify(layer.patterns),\n        layer.metadata ? JSON.stringify(layer.metadata) : null,\n        layer.updatedAt,\n      ]\n    );\n  }\n\n  upsertArchFilePackage(filePath: string, packageId: string): void {\n    this.db.run(\n      'INSERT OR IGNORE INTO arch_file_packages (file_path, package_id) VALUES (?,?)',\n      [filePath, packageId]\n    );\n  }\n\n  upsertArchFileLayer(filePath: string, layerId: string, confidence: number, matchedPattern: string): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence, matched_pattern)\n       VALUES (?,?,?,?)`,\n      [filePath, layerId, confidence, matchedPattern]\n    );\n  }\n\n  upsertArchPackageDep(sourcePkg: string, targetPkg: string, depCount: number, files?: Array<{ from: string; to: string }>): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_package_deps (source_pkg, target_pkg, dep_count, files)\n       VALUES (?,?,?,?)`,\n      [sourcePkg, targetPkg, depCount, files ? JSON.stringify(files) : null]\n    );\n  }\n\n  upsertArchLayerDep(sourceLayer: string, targetLayer: string, depCount: number): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_layer_deps (source_layer, target_layer, dep_count)\n       VALUES (?,?,?)`,\n      [sourceLayer, targetLayer, depCount]\n    );\n  }\n\n  upsertArchCoupling(coupling: ArchCoupling): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_coupling (package_id, afferent, efferent, instability, updated_at)\n       VALUES (?,?,?,?,?)`,\n      [coupling.packageId, coupling.afferent, coupling.efferent, coupling.instability, coupling.updatedAt]\n    );\n  }\n\n  getArchPackages(): ArchPackage[] {\n    return this.db.all('SELECT * FROM arch_packages').map((r: any): ArchPackage => ({\n      id: r.id,\n      name: r.name,\n      path: r.path,\n      source: r.source,\n      language: r.language ?? undefined,\n      manifestPath: r.manifest_path ?? undefined,\n      version: r.version ?? undefined,\n      externalDeps: r.external_deps ? JSON.parse(r.external_deps) : undefined,\n      metadata: r.metadata ? JSON.parse(r.metadata) : undefined,\n      updatedAt: r.updated_at,\n    }));\n  }\n\n  getArchLayers(): ArchLayer[] {\n    return this.db.all('SELECT * FROM arch_layers').map((r: any): ArchLayer => ({\n      id: r.id,\n      name: r.name,\n      source: r.source,\n      patterns: JSON.parse(r.patterns),\n      metadata: r.metadata ? JSON.parse(r.metadata) : undefined,\n      updatedAt: r.updated_at,\n    }));\n  }\n\n  getArchPackageDeps(): ArchPackageDep[] {\n    return this.db.all('SELECT * FROM arch_package_deps').map((r: any): ArchPackageDep => ({\n      sourcePkg: r.source_pkg,\n      targetPkg: r.target_pkg,\n      depCount: r.dep_count,\n      files: r.files ? JSON.parse(r.files) : undefined,\n    }));\n  }\n\n  getArchLayerDeps(): ArchLayerDep[] {\n    return this.db.all('SELECT * FROM arch_layer_deps').map((r: any): ArchLayerDep => ({\n      sourceLayer: r.source_layer,\n      targetLayer: r.target_layer,\n      depCount: r.dep_count,\n    }));\n  }\n\n  getArchCoupling(): ArchCoupling[] {\n    return this.db.all('SELECT * FROM arch_coupling').map((r: any): ArchCoupling => ({\n      packageId: r.package_id,\n      afferent: r.afferent,\n      efferent: r.efferent,\n      instability: r.instability,\n      updatedAt: r.updated_at,\n    }));\n  }\n\n  getArchStats(): { packages: number; layers: number; packageDeps: number } {\n    return {\n      packages: this.db.get('SELECT COUNT(*) as c FROM arch_packages')?.c ?? 0,\n      layers: this.db.get('SELECT COUNT(*) as c FROM arch_layers')?.c ?? 0,\n      packageDeps: this.db.get('SELECT COUNT(*) as c FROM arch_package_deps')?.c ?? 0,\n    };\n  }\n\n  /**\n   * Return file-to-file import relationships by joining edges + nodes.\n   * Used by ArchitectureAnalyzer to roll up package-level dependencies.\n   */\n  getFileImportPairs(): Array<{ sourceFile: string; targetFile: string }> {\n    return this.db.all(\n      `SELECT DISTINCT n1.file_path as source_file, n2.file_path as target_file\n       FROM edges e\n       JOIN nodes n1 ON n1.id = e.source\n       JOIN nodes n2 ON n2.id = e.target\n       WHERE e.kind = 'imports' AND n1.file_path != n2.file_path`\n    ).map((r: any) => ({ sourceFile: r.source_file, targetFile: r.target_file }));\n  }\n\n  getArchFilePackages(): Array<{ filePath: string; packageId: string }> {\n    return this.db.all('SELECT file_path, package_id FROM arch_file_packages')\n      .map((r: any) => ({ filePath: r.file_path, packageId: r.package_id }));\n  }\n\n  getArchFileLayers(): Array<{ filePath: string; layerId: string; confidence: number; matchedPattern: string }> {\n    return this.db.all('SELECT file_path, layer_id, confidence, matched_pattern FROM arch_file_layers')\n      .map((r: any) => ({\n        filePath: r.file_path,\n        layerId: r.layer_id,\n        confidence: r.confidence,\n        matchedPattern: r.matched_pattern,\n      }));\n  }\n\n  getArchitectureResult(): {\n    packages: ArchPackage[];\n    layers: ArchLayer[];\n    packageDeps: ArchPackageDep[];\n    layerDeps: ArchLayerDep[];\n    coupling: ArchCoupling[];\n  } {\n    return {\n      packages: this.getArchPackages(),\n      layers: this.getArchLayers(),\n      packageDeps: this.getArchPackageDeps(),\n      layerDeps: this.getArchLayerDeps(),\n      coupling: this.getArchCoupling(),\n    };\n  }\n\n  // \u2500\u2500 Transactions \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  transaction<T>(fn: () => T): T {\n    this.db.run('BEGIN');\n    try {\n      const result = fn();\n      this.db.run('COMMIT');\n      return result;\n    } catch (err) {\n      this.db.run('ROLLBACK');\n      throw err;\n    }\n  }\n\n  close(): void {\n    this.db.close();\n  }\n}\n"],
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+  "sourcesContent": ["/**\n * KiroGraph Database Layer\n * Wraps node-sqlite3-wasm for portability (no native bindings needed).\n */\n\nimport * as path from 'path';\nimport * as fs from 'fs';\nimport type { Node, Edge, FileRecord, NodeKind, Language, GraphStats, NodeContext, NodeMetrics, SearchOptions } from '../types';\nimport type { ArchPackage, ArchLayer, ArchPackageDep, ArchLayerDep, ArchCoupling } from '../architecture/types';\n\n// eslint-disable-next-line @typescript-eslint/no-require-imports\nconst { Database } = require('node-sqlite3-wasm');\n\nconst CURRENT_SCHEMA_VERSION = 1;\n\nexport class GraphDatabase {\n  private db: any;\n  private projectRoot: string;\n\n  constructor(projectRoot: string) {\n    this.projectRoot = projectRoot;\n    const dbDir = path.join(projectRoot, '.kirograph');\n    fs.mkdirSync(dbDir, { recursive: true });\n    const dbPath = path.join(dbDir, 'kirograph.db');\n\n    // \u2500\u2500 Pre-flight lock 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\n    // node-sqlite3-wasm calls process.abort() when the DB is locked, producing\n    // a cryptic \"Aborted()\" with no context. Detect the lock file early and\n    // throw a clean error instead so the global handler can surface it clearly.\n    const lockPath = path.join(dbDir, 'kirograph.db.lock');\n    if (fs.existsSync(lockPath)) {\n      throw new Error(\n        `Database is locked by another process (${lockPath} exists).\\n` +\n        `Run: kirograph unlock\\n` +\n        `Or delete the lock manually: ${lockPath}`\n      );\n    }\n\n    this.db = new Database(dbPath);\n    this.db.exec(`\n      PRAGMA journal_mode=WAL;\n      PRAGMA foreign_keys=ON;\n      PRAGMA busy_timeout=120000;\n      PRAGMA synchronous=NORMAL;\n      PRAGMA cache_size=-64000;\n      PRAGMA temp_store=MEMORY;\n      PRAGMA mmap_size=268435456;\n    `);\n    this.applySchema();\n  }\n\n  private applySchema(): void {\n    const schemaPath = path.join(__dirname, '../db/schema.sql');\n    const sql = fs.readFileSync(schemaPath, 'utf8');\n    this.db.exec(sql);\n    this.runMigrations();\n  }\n\n  /**\n   * Apply memory schema tables. Called when enableMemory is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyMemorySchema(): void {\n    const schemaPath = path.join(__dirname, '../db/memory-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n  }\n\n  /**\n   * Apply docs schema tables. Called when enableDocs is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyDocsSchema(): void {\n    const schemaPath = path.join(__dirname, '../db/docs-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n  }\n\n  /**\n   * Apply data schema tables. Called when enableData is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyDataSchema(): void {\n    const schemaPath = path.join(__dirname, '../db/data-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n    // Migrate existing DBs: add columns introduced after initial release.\n    const tryAlter = (stmt: string) => { try { this.db.run(stmt); } catch { /* already exists */ } };\n    tryAlter('ALTER TABLE data_datasets ADD COLUMN metadata_json TEXT');\n  }\n\n  /**\n   * Apply patterns schema tables. Called when enablePatterns is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyPatternsSchema(): void {\n    const schemaPath = path.join(__dirname, '../db/patterns-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n    // Migrate existing DBs: add new columns introduced after initial release.\n    const tryAlter = (stmt: string) => { try { this.db.run(stmt); } catch { /* already exists */ } };\n    tryAlter('ALTER TABLE pattern_matches ADD COLUMN symbol_node_id TEXT');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_pm_symbol ON pattern_matches(symbol_node_id)');\n  }\n\n  /**\n   * Apply security schema tables. Called when enableSecurity is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applySecuritySchema(): void {\n    const schemaPath = path.join(__dirname, '../db/security-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n    // Migrate existing DBs: add new columns introduced after initial release.\n    const tryAlter = (stmt: string) => { try { this.db.run(stmt); } catch { /* already exists */ } };\n    tryAlter('ALTER TABLE sec_dependencies ADD COLUMN license TEXT');\n    tryAlter('ALTER TABLE sec_dependencies ADD COLUMN latest_version TEXT');\n    tryAlter('ALTER TABLE sec_dependencies ADD COLUMN latest_published INTEGER');\n    tryAlter('ALTER TABLE sec_dependencies ADD COLUMN staleness_score REAL');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN epss_score REAL');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN epss_percentile REAL');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN epss_fetched_at INTEGER');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_sec_deps_license ON sec_dependencies(license)');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_sec_deps_staleness ON sec_dependencies(staleness_score)');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_sec_vulns_epss ON sec_vulnerabilities(epss_score)');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN risk_score REAL');\n    tryAlter('CREATE INDEX IF NOT EXISTS idx_sec_vulns_risk ON sec_vulnerabilities(risk_score)');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN first_detected_at INTEGER');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN fix_available_since INTEGER');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN suppressed_at INTEGER');\n    tryAlter('ALTER TABLE sec_vulnerabilities ADD COLUMN remediated_at INTEGER');\n  }\n\n  /**\n   * Apply wiki schema tables. Called when enableWiki is true.\n   * Safe to call multiple times (CREATE IF NOT EXISTS).\n   */\n  applyWikiSchema(): void {\n    const schemaPath = path.join(__dirname, '../db/wiki-schema.sql');\n    if (fs.existsSync(schemaPath)) {\n      const sql = fs.readFileSync(schemaPath, 'utf8');\n      this.db.exec(sql);\n    }\n  }\n\n  /**\n   * Get the raw database handle (for MemoryDatabase).\n   */\n  getRawDb(): any {\n    return this.db;\n  }\n\n  private runMigrations(): void {\n    // Record initial schema version if not present\n    const versionRow = this.db.get('SELECT version FROM schema_versions ORDER BY version DESC LIMIT 1');\n    const currentVersion = versionRow ? versionRow.version : 0;\n\n    if (currentVersion < CURRENT_SCHEMA_VERSION) {\n      // Migration 1: schema.sql now includes all columns \u2014 nothing extra needed.\n      // The schema CREATE IF NOT EXISTS statements handle initial setup.\n      this.db.run('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)',\n        [CURRENT_SCHEMA_VERSION, Date.now()]);\n    }\n\n    // Add attempted_strategies column to unresolved_refs if not present.\n    // SQLite throws if the column already exists, so we catch that error.\n    try {\n      this.db.run('ALTER TABLE unresolved_refs ADD COLUMN attempted_strategies TEXT');\n    } catch {\n      // Column already exists \u2014 nothing to do.\n    }\n\n    // Add confidence columns to edges if not present.\n    try {\n      this.db.run(\"ALTER TABLE edges ADD COLUMN confidence TEXT NOT NULL DEFAULT 'extracted'\");\n    } catch {\n      // Column already exists \u2014 nothing to do.\n    }\n    try {\n      this.db.run('ALTER TABLE edges ADD COLUMN confidence_score REAL NOT NULL DEFAULT 1.0');\n    } catch {\n      // Column already exists \u2014 nothing to do.\n    }\n  }\n\n  // \u2500\u2500 Files \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  upsertFile(record: FileRecord): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO files (path, content_hash, language, file_size, symbol_count, indexed_at)\n       VALUES (?, ?, ?, ?, ?, ?)`,\n      [record.path, record.contentHash, record.language, record.fileSize, record.symbolCount, record.indexedAt]\n    );\n  }\n\n  getFile(filePath: string): FileRecord | null {\n    const row = this.db.get('SELECT * FROM files WHERE path = ?', [filePath]);\n    return row ? this.rowToFile(row) : null;\n  }\n\n  getAllFiles(): FileRecord[] {\n    return this.db.all('SELECT * FROM files').map(this.rowToFile);\n  }\n\n  deleteFile(filePath: string): void {\n    // Cascade deletes nodes (and their edges via FK)\n    this.db.run('DELETE FROM nodes WHERE file_path = ?', [filePath]);\n    this.db.run('DELETE FROM files WHERE path = ?', [filePath]);\n  }\n\n  private rowToFile(row: any): FileRecord {\n    return {\n      path: row.path,\n      contentHash: row.content_hash,\n      language: row.language as Language,\n      fileSize: row.file_size,\n      symbolCount: row.symbol_count,\n      indexedAt: row.indexed_at,\n    };\n  }\n\n  // \u2500\u2500 Nodes \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  upsertNode(node: Node): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO nodes\n        (id, kind, name, qualified_name, file_path, language,\n         start_line, end_line, start_column, end_column,\n         docstring, signature, visibility,\n         is_exported, is_async, is_static, is_abstract,\n         decorators, type_parameters, updated_at)\n       VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)`,\n      [\n        node.id, node.kind, node.name, node.qualifiedName, node.filePath, node.language,\n        node.startLine, node.endLine, node.startColumn, node.endColumn,\n        node.docstring ?? null, node.signature ?? null, node.visibility ?? null,\n        node.isExported ? 1 : 0, node.isAsync ? 1 : 0,\n        node.isStatic ? 1 : 0, node.isAbstract ? 1 : 0,\n        node.decorators ? JSON.stringify(node.decorators) : null,\n        node.typeParameters ? JSON.stringify(node.typeParameters) : null,\n        node.updatedAt,\n      ]\n    );\n    // Keep FTS in sync\n    this.db.run(\n      `INSERT OR REPLACE INTO nodes_fts (id, name, qualified_name, docstring, signature)\n       VALUES (?, ?, ?, ?, ?)`,\n      [node.id, node.name, node.qualifiedName, node.docstring ?? '', node.signature ?? '']\n    );\n  }\n\n  getNode(id: string): Node | null {\n    const row = this.db.get('SELECT * FROM nodes WHERE id = ?', [id]);\n    return row ? this.rowToNode(row) : null;\n  }\n\n  getNodesByFile(filePath: string): Node[] {\n    return this.db.all('SELECT * FROM nodes WHERE file_path = ?', [filePath]).map(this.rowToNode);\n  }\n\n  getNodesByKind(kind: Node['kind']): Node[] {\n    return this.db.all('SELECT * FROM nodes WHERE kind = ?', [kind]).map(this.rowToNode);\n  }\n\n  findNodesByExactName(name: string, kinds?: NodeKind[], limit = 20): Node[] {\n    if (kinds && kinds.length > 0) {\n      const placeholders = kinds.map(() => '?').join(',');\n      return this.db.all(\n        `SELECT * FROM nodes WHERE name = ? AND kind IN (${placeholders}) LIMIT ?`,\n        [name, ...kinds, limit]\n      ).map(this.rowToNode);\n    }\n    return this.db.all(\n      'SELECT * FROM nodes WHERE name = ? LIMIT ?',\n      [name, limit]\n    ).map(this.rowToNode);\n  }\n\n  searchNodes(query: string, opts: SearchOptions = {}): Node[] {\n    const { kinds, languages, limit = 20 } = opts;\n    // Sanitize for FTS5: strip special chars and append wildcard.\n    // Both the MATCH value and LIMIT are inlined (not bound via ?) because\n    // node-sqlite3-wasm passes bound parameters through to FTS5's own query\n    // parser before SQLite substitutes them, causing \"syntax error near ?\".\n    const safe = query\n      .replace(/\\b(AND|OR|NOT)\\b/g, ' ')       // FTS5 boolean operators\n      .replace(/['\"*()?\\-+^~:{}\\\\\\.\\/,]/g, ' ')  // FTS5 special chars (incl. / and ,)\n      .replace(/\\s+/g, ' ')\n      .trim();\n    if (!safe) return [];\n\n    const ftsQuery = safe + '*';\n    const safeLimit = Math.max(1, Math.floor(Number(limit)));\n\n    const conditions: string[] = [];\n    const params: any[] = [];\n\n    if (kinds && kinds.length > 0) {\n      conditions.push(`kind IN (${kinds.map(() => '?').join(',')})`);\n      params.push(...kinds);\n    }\n    if (languages && languages.length > 0) {\n      conditions.push(`language IN (${languages.map(() => '?').join(',')})`);\n      params.push(...languages);\n    }\n\n    const where = conditions.length > 0 ? `AND ${conditions.join(' AND ')}` : '';\n\n    return this.db.all(\n      `SELECT * FROM nodes\n       WHERE id IN (SELECT rowid FROM nodes_fts WHERE nodes_fts MATCH '${ftsQuery}')\n       ${where}\n       LIMIT ${safeLimit}`,\n      params\n    ).map(this.rowToNode);\n  }\n\n  searchNodesByName(name: string, opts: SearchOptions = {}): Node[] {\n    const { kinds, languages, limit = 20 } = opts;\n    const pattern = `%${name}%`;\n    const conditions: string[] = ['name LIKE ?'];\n    const params: any[] = [pattern];\n\n    if (kinds && kinds.length > 0) {\n      conditions.push(`kind IN (${kinds.map(() => '?').join(',')})`);\n      params.push(...kinds);\n    }\n    if (languages && languages.length > 0) {\n      conditions.push(`language IN (${languages.map(() => '?').join(',')})`);\n      params.push(...languages);\n    }\n    params.push(limit);\n\n    return this.db.all(\n      `SELECT * FROM nodes WHERE ${conditions.join(' AND ')} LIMIT ?`,\n      params\n    ).map(this.rowToNode);\n  }\n\n  deleteNodesByFile(filePath: string): void {\n    const ids = this.db.all('SELECT id FROM nodes WHERE file_path = ?', [filePath]).map((r: any) => r.id);\n    if (ids.length === 0) return;\n    const placeholders = ids.map(() => '?').join(',');\n    this.db.run(`DELETE FROM edges WHERE source IN (${placeholders}) OR target IN (${placeholders})`, [...ids, ...ids]);\n    this.db.run(`DELETE FROM nodes_fts WHERE id IN (${placeholders})`, ids);\n    this.db.run(`DELETE FROM nodes WHERE file_path = ?`, [filePath]);\n  }\n\n  private rowToNode(row: any): Node {\n    return {\n      id: row.id,\n      kind: row.kind as NodeKind,\n      name: row.name,\n      qualifiedName: row.qualified_name,\n      filePath: row.file_path,\n      language: row.language as Language,\n      startLine: row.start_line,\n      endLine: row.end_line,\n      startColumn: row.start_column,\n      endColumn: row.end_column,\n      docstring: row.docstring ?? undefined,\n      signature: row.signature ?? undefined,\n      visibility: row.visibility ?? undefined,\n      isExported: row.is_exported === 1,\n      isAsync: row.is_async === 1,\n      isStatic: row.is_static === 1,\n      isAbstract: row.is_abstract === 1,\n      decorators: row.decorators ? JSON.parse(row.decorators) : undefined,\n      typeParameters: row.type_parameters ? JSON.parse(row.type_parameters) : undefined,\n      updatedAt: row.updated_at,\n    };\n  }\n\n  // \u2500\u2500 Edges \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  insertEdge(edge: Edge): void {\n    this.db.run(\n      `INSERT OR IGNORE INTO edges (source, target, kind, metadata, line, column, confidence, confidence_score)\n       VALUES (?, ?, ?, ?, ?, ?, ?, ?)`,\n      [edge.source, edge.target, edge.kind, edge.metadata ? JSON.stringify(edge.metadata) : null, edge.line ?? null, edge.column ?? null, edge.confidence ?? 'extracted', edge.confidenceScore ?? 1.0]\n    );\n  }\n\n  getCallers(nodeId: string, limit = 30): Node[] {\n    return this.db.all(\n      `SELECT n.* FROM nodes n\n       JOIN edges e ON e.source = n.id\n       WHERE e.target = ? AND e.kind = 'calls'\n       LIMIT ?`,\n      [nodeId, limit]\n    ).map(this.rowToNode);\n  }\n\n  getCallees(nodeId: string, limit = 30): Node[] {\n    return this.db.all(\n      `SELECT n.* FROM nodes n\n       JOIN edges e ON e.target = n.id\n       WHERE e.source = ? AND e.kind = 'calls'\n       LIMIT ?`,\n      [nodeId, limit]\n    ).map(this.rowToNode);\n  }\n\n  getImpactRadius(nodeId: string, depth = 2): Node[] {\n    // BFS over 'calls' and 'imports' edges (dependents)\n    const visited = new Set<string>([nodeId]);\n    let frontier = [nodeId];\n    for (let d = 0; d < depth; d++) {\n      if (frontier.length === 0) break;\n      const placeholders = frontier.map(() => '?').join(',');\n      const rows = this.db.all(\n        `SELECT DISTINCT source FROM edges WHERE target IN (${placeholders}) AND kind IN ('calls','imports')`,\n        frontier\n      );\n      frontier = [];\n      for (const row of rows) {\n        if (!visited.has(row.source)) {\n          visited.add(row.source);\n          frontier.push(row.source);\n        }\n      }\n    }\n    visited.delete(nodeId);\n    if (visited.size === 0) return [];\n    const ids = [...visited];\n    const placeholders = ids.map(() => '?').join(',');\n    return this.db.all(`SELECT * FROM nodes WHERE id IN (${placeholders})`, ids).map(this.rowToNode);\n  }\n\n  getEdgesForNodes(nodeIds: string[]): Edge[] {\n    if (nodeIds.length === 0) return [];\n    const placeholders = nodeIds.map(() => '?').join(',');\n    return this.db.all(\n      `SELECT * FROM edges WHERE source IN (${placeholders}) OR target IN (${placeholders})`,\n      [...nodeIds, ...nodeIds]\n    ).map((row: any) => ({\n      source: row.source,\n      target: row.target,\n      kind: row.kind,\n      metadata: row.metadata ? JSON.parse(row.metadata) : undefined,\n      line: row.line ?? undefined,\n      column: row.column ?? undefined,\n    }));\n  }\n\n  /**\n   * Find files that import (depend on) the given file path.\n   * Used for affected-test traversal.\n   */\n  getDependentFiles(filePath: string): string[] {\n    // Find nodes in the target file\n    const targetNodes = this.db.all('SELECT id FROM nodes WHERE file_path = ?', [filePath]);\n    if (targetNodes.length === 0) return [];\n    const ids = targetNodes.map((r: any) => r.id);\n    const placeholders = ids.map(() => '?').join(',');\n    // Find source nodes that call/import these target nodes\n    const rows = this.db.all(\n      `SELECT DISTINCT n.file_path FROM nodes n\n       JOIN edges e ON e.source = n.id\n       WHERE e.target IN (${placeholders}) AND e.kind IN ('calls','imports')\n       AND n.file_path != ?`,\n      [...ids, filePath]\n    );\n    return rows.map((r: any) => r.file_path);\n  }\n\n  // \u2500\u2500 Unresolved References \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  insertUnresolvedRef(sourceId: string, refName: string, refKind: string, filePath: string, line?: number, column?: number): void {\n    this.db.run(\n      `INSERT INTO unresolved_refs (source_id, ref_name, ref_kind, file_path, line, column)\n       VALUES (?, ?, ?, ?, ?, ?)`,\n      [sourceId, refName, refKind, filePath, line ?? null, column ?? null]\n    );\n  }\n\n  deleteUnresolvedRefsByFile(filePath: string): void {\n    this.db.run('DELETE FROM unresolved_refs WHERE file_path = ?', [filePath]);\n  }\n\n  /**\n   * Resolve pending references:\n   * - refKind='function': 3-strategy name matching \u2192 'calls' edge\n   * - refKind='import': path-based resolution \u2192 'imports' edge\n   *\n   * Returns the number of edges successfully created.\n   */\n  resolveUnresolvedRefs(): number {\n    const refs = this.db.all('SELECT * FROM unresolved_refs');\n    let resolved = 0;\n\n    for (const ref of refs) {\n      const { id: refId, source_id: sourceId, ref_name: refName, ref_kind: refKind, file_path: filePath, line, column } = ref;\n\n      if (refKind === 'function') {\n        // Strategy 1: exact name match\n        let target = this.db.get('SELECT id FROM nodes WHERE name = ? LIMIT 1', [refName]);\n        let confidence: 'extracted' | 'inferred' | 'ambiguous' = 'inferred';\n        let confidenceScore = 1.0;\n\n        // Strategy 2: qualified name suffix\n        if (!target) {\n          target = this.db.get(\n            `SELECT id FROM nodes WHERE qualified_name LIKE ? LIMIT 1`,\n            [`%::${refName}`]\n          );\n        }\n\n        // Strategy 3: case-insensitive\n        if (!target) {\n          target = this.db.get(\n            'SELECT id FROM nodes WHERE lower(name) = lower(?) LIMIT 1',\n            [refName]\n          );\n          // Case-insensitive match is less certain\n          if (target) confidenceScore = 0.8;\n        }\n\n        // Check if there are multiple candidates (ambiguous)\n        if (target) {\n          const candidateCount = this.db.get('SELECT COUNT(*) as cnt FROM nodes WHERE name = ?', [refName]);\n          if (candidateCount && candidateCount.cnt > 1) {\n            confidence = 'ambiguous';\n            confidenceScore = 1.0 / candidateCount.cnt;\n          }\n        }\n\n        if (target) {\n          this.insertEdge({ source: sourceId, target: target.id, kind: 'calls', line: line ?? undefined, column: column ?? undefined, confidence, confidenceScore });\n          this.db.run('DELETE FROM unresolved_refs WHERE id = ?', [refId]);\n          resolved++;\n        }\n      } else if (refKind === 'import') {\n        // Resolve import path to an indexed file\n        const targetFileNode = this.resolveImportPath(refName, filePath);\n        if (targetFileNode) {\n          this.insertEdge({ source: sourceId, target: targetFileNode, kind: 'imports', line: line ?? undefined, column: column ?? undefined, confidence: 'inferred', confidenceScore: 1.0 });\n          this.db.run('DELETE FROM unresolved_refs WHERE id = ?', [refId]);\n          resolved++;\n        }\n      }\n    }\n\n    return resolved;\n  }\n\n  /** @deprecated Use resolveUnresolvedRefs() */\n  resolveCallEdges(): number {\n    return this.resolveUnresolvedRefs();\n  }\n\n  /**\n   * Resolve a module import path to the ID of the first node in the target file.\n   * Returns null if no indexed file matches.\n   */\n  private resolveImportPath(importPath: string, sourceFilePath: string): string | null {\n    // Only resolve relative imports\n    if (!importPath.startsWith('.')) return null;\n\n    const sourceDir = sourceFilePath.replace(/[^/]+$/, '');\n    // Normalize the relative path\n    const segments = (sourceDir + importPath).split('/');\n    const normalized: string[] = [];\n    for (const seg of segments) {\n      if (seg === '..') normalized.pop();\n      else if (seg !== '.') normalized.push(seg);\n    }\n    const basePath = normalized.join('/');\n\n    // Try exact match, then with common extensions\n    const candidates = [\n      basePath,\n      basePath + '.ts',\n      basePath + '.tsx',\n      basePath + '.js',\n      basePath + '.jsx',\n      basePath + '/index.ts',\n      basePath + '/index.tsx',\n      basePath + '/index.js',\n    ];\n\n    for (const candidate of candidates) {\n      const row = this.db.get('SELECT id FROM nodes WHERE file_path = ? LIMIT 1', [candidate]);\n      if (row) return row.id;\n    }\n\n    return null;\n  }\n\n  // \u2500\u2500 Node Context & Metrics \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  getNodeContext(nodeId: string): NodeContext | null {\n    const node = this.getNode(nodeId);\n    if (!node) return null;\n\n    const ancestors = this.db.all(\n      `SELECT n.* FROM nodes n\n       JOIN edges e ON e.target = n.id\n       WHERE e.source = ? AND e.kind = 'contains'`,\n      [nodeId]\n    ).map(this.rowToNode);\n\n    const children = this.db.all(\n      `SELECT n.* FROM nodes n\n       JOIN edges e ON e.source = n.id\n       WHERE e.target = n.id AND e.source = ? AND e.kind = 'contains'`,\n      [nodeId]\n    ).map(this.rowToNode);\n\n    const callers = this.getCallers(nodeId, 20);\n    const callees = this.getCallees(nodeId, 20);\n\n    return { node, ancestors, children, callers, callees };\n  }\n\n  getNodeMetrics(nodeId: string): NodeMetrics {\n    const incomingEdgeCount = (this.db.get('SELECT COUNT(*) as c FROM edges WHERE target = ?', [nodeId])?.c ?? 0);\n    const outgoingEdgeCount = (this.db.get('SELECT COUNT(*) as c FROM edges WHERE source = ?', [nodeId])?.c ?? 0);\n    const callCount = (this.db.get(`SELECT COUNT(*) as c FROM edges WHERE source = ? AND kind = 'calls'`, [nodeId])?.c ?? 0);\n    const callerCount = (this.db.get(`SELECT COUNT(*) as c FROM edges WHERE target = ? AND kind = 'calls'`, [nodeId])?.c ?? 0);\n    const childCount = (this.db.get(`SELECT COUNT(*) as c FROM edges WHERE source = ? AND kind = 'contains'`, [nodeId])?.c ?? 0);\n    return { incomingEdgeCount, outgoingEdgeCount, callCount, callerCount, childCount };\n  }\n\n  // \u2500\u2500 Graph Analysis \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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   * Find symbols with no incoming edges (potential dead code).\n   * Excludes exported symbols since they may be consumed externally.\n   */\n  findDeadCode(limit = 50): Node[] {\n    return this.db.all(\n      `SELECT * FROM nodes\n       WHERE kind IN ('function','method','class')\n         AND is_exported = 0\n         AND id NOT IN (SELECT DISTINCT target FROM edges)\n       LIMIT ?`,\n      [limit]\n    ).map(this.rowToNode);\n  }\n\n  /**\n   * Find circular import dependencies using DFS over import edges.\n   * Returns arrays of file paths forming cycles.\n   */\n  findCircularDependencies(): string[][] {\n    // Build adjacency map: file \u2192 imported files\n    const rows = this.db.all(\n      `SELECT DISTINCT n1.file_path as src, n2.file_path as dst\n       FROM edges e\n       JOIN nodes n1 ON n1.id = e.source\n       JOIN nodes n2 ON n2.id = e.target\n       WHERE e.kind = 'imports' AND n1.file_path != n2.file_path`\n    );\n\n    const adj = new Map<string, Set<string>>();\n    for (const row of rows) {\n      if (!adj.has(row.src)) adj.set(row.src, new Set());\n      adj.get(row.src)!.add(row.dst);\n    }\n\n    const cycles: string[][] = [];\n    const visited = new Set<string>();\n    const pathSet = new Set<string>();\n    const pathArr: string[] = [];\n\n    function dfs(node: string): void {\n      if (pathSet.has(node)) {\n        const cycleStart = pathArr.indexOf(node);\n        cycles.push(pathArr.slice(cycleStart).concat(node));\n        return;\n      }\n      if (visited.has(node)) return;\n      visited.add(node);\n      pathSet.add(node);\n      pathArr.push(node);\n      for (const neighbor of adj.get(node) ?? []) {\n        dfs(neighbor);\n      }\n      pathArr.pop();\n      pathSet.delete(node);\n    }\n\n    for (const node of adj.keys()) {\n      if (!visited.has(node)) dfs(node);\n    }\n\n    return cycles;\n  }\n\n  /**\n   * Find the shortest path between two nodes via directed BFS (outgoing edges only).\n   */\n  findPath(fromId: string, toId: string, maxDepth = 10): Node[] {\n    if (fromId === toId) {\n      const node = this.getNode(fromId);\n      return node ? [node] : [];\n    }\n\n    const prev = new Map<string, string>();\n    const queue: string[] = [fromId];\n    const visited = new Set<string>([fromId]);\n    let depth = 0;\n\n    outer: while (queue.length > 0 && depth < maxDepth) {\n      const levelSize = queue.length;\n      depth++;\n      for (let i = 0; i < levelSize; i++) {\n        const current = queue.shift()!;\n        // Directed: only follow outgoing edges\n        const rows = this.db.all(\n          `SELECT DISTINCT target as next FROM edges WHERE source = ?`,\n          [current]\n        );\n        for (const row of rows) {\n          if (!visited.has(row.next)) {\n            visited.add(row.next);\n            prev.set(row.next, current);\n            if (row.next === toId) break outer;\n            queue.push(row.next);\n          }\n        }\n      }\n    }\n\n    if (!prev.has(toId)) return [];\n\n    // Reconstruct path\n    const pathIds: string[] = [];\n    let cur: string | undefined = toId;\n    while (cur !== undefined) {\n      pathIds.unshift(cur);\n      cur = prev.get(cur);\n    }\n\n    const result: Node[] = [];\n    for (const id of pathIds) {\n      const node = this.getNode(id);\n      if (node) result.push(node);\n    }\n    return result;\n  }\n\n  /**\n   * Traverse type hierarchy via 'extends' and 'implements' edges.\n   * direction 'up' = base types, 'down' = derived types, 'both' = all.\n   */\n  getTypeHierarchy(nodeId: string, direction: 'up' | 'down' | 'both' = 'both'): Node[] {\n    const visited = new Set<string>([nodeId]);\n    const frontier = [nodeId];\n    const result: Node[] = [];\n\n    while (frontier.length > 0) {\n      const current = frontier.shift()!;\n      let rows: any[] = [];\n\n      if (direction === 'up' || direction === 'both') {\n        // current extends/implements something \u2192 go up\n        const up = this.db.all(\n          `SELECT target as id FROM edges WHERE source = ? AND kind IN ('extends','implements')`,\n          [current]\n        );\n        rows = rows.concat(up);\n      }\n      if (direction === 'down' || direction === 'both') {\n        // something extends/implements current \u2192 go down\n        const down = this.db.all(\n          `SELECT source as id FROM edges WHERE target = ? AND kind IN ('extends','implements')`,\n          [current]\n        );\n        rows = rows.concat(down);\n      }\n\n      for (const row of rows) {\n        if (!visited.has(row.id)) {\n          visited.add(row.id);\n          frontier.push(row.id);\n          const node = this.getNode(row.id);\n          if (node) result.push(node);\n        }\n      }\n    }\n\n    return result;\n  }\n\n  // \u2500\u2500 Stats \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  getEmbeddingCount(): number {\n    try {\n      const row = this.db.get('SELECT COUNT(*) as c FROM vectors');\n      return row ? row.c : 0;\n    } catch {\n      return 0;\n    }\n  }\n\n  storeEmbedding(nodeId: string, embedding: Float32Array, model: string): void {\n    const buf = Buffer.from(embedding.buffer);\n    this.db.run(\n      `INSERT OR REPLACE INTO vectors (node_id, embedding, model, created_at) VALUES (?, ?, ?, ?)`,\n      [nodeId, buf, model, Date.now()]\n    );\n  }\n\n  getEmbeddedNodeIds(): string[] {\n    return this.db.all('SELECT node_id FROM vectors').map((r: any) => r.node_id);\n  }\n\n  getAllEmbeddings(): Array<{ nodeId: string; embedding: Float32Array }> {\n    const rows = this.db.all('SELECT node_id, embedding FROM vectors');\n    return rows.map((r: any) => ({\n      nodeId: r.node_id as string,\n      embedding: new Float32Array(\n        (r.embedding as Buffer).buffer,\n        (r.embedding as Buffer).byteOffset,\n        (r.embedding as Buffer).byteLength / 4\n      ),\n    }));\n  }\n\n  getAllNodes(): import('../types').Node[] {\n    return this.db.all('SELECT * FROM nodes').map(this.rowToNode);\n  }\n\n  /**\n   * Returns embeddable nodes in pages for memory-efficient streaming.\n   * `kinds` filters by node kind (e.g. ['function','method','class']).\n   * Returns an empty array when offset >= total count.\n   */\n  getEmbeddableNodesPaged(kinds: string[], limit: number, offset: number): import('../types').Node[] {\n    if (kinds.length === 0) return [];\n    const placeholders = kinds.map(() => '?').join(',');\n    return this.db.all(\n      `SELECT * FROM nodes WHERE kind IN (${placeholders}) LIMIT ? OFFSET ?`,\n      [...kinds, limit, offset]\n    ).map(this.rowToNode);\n  }\n\n  /** Count of nodes whose kind is in the provided list. */\n  countEmbeddableNodes(kinds: string[]): number {\n    if (kinds.length === 0) return 0;\n    const placeholders = kinds.map(() => '?').join(',');\n    const row = this.db.get(`SELECT COUNT(*) as c FROM nodes WHERE kind IN (${placeholders})`, kinds);\n    return row?.c ?? 0;\n  }\n\n  getAllEdges(): Edge[] {\n    return this.db.all('SELECT source, target, kind FROM edges').map((row: any) => ({\n      source: row.source,\n      target: row.target,\n      kind: row.kind,\n    }));\n  }\n\n  /**\n   * Find the top-N most-connected nodes by total edge degree (in + out).\n   * Excludes 'contains' edges (structural nesting, not semantic connections).\n   */\n  findHotspots(limit = 20): Array<Node & { degree: number; inDegree: number; outDegree: number }> {\n    const rows = this.db.all(\n      `SELECT n.*,\n         (SELECT COUNT(*) FROM edges WHERE target = n.id AND kind != 'contains') AS in_degree,\n         (SELECT COUNT(*) FROM edges WHERE source = n.id AND kind != 'contains') AS out_degree,\n         (SELECT COUNT(*) FROM edges WHERE (source = n.id OR target = n.id) AND kind != 'contains') AS degree\n       FROM nodes n\n       ORDER BY degree DESC\n       LIMIT ?`,\n      [limit]\n    );\n    return rows.map((row: any) => ({\n      ...this.rowToNode(row),\n      degree: row.degree as number,\n      inDegree: row.in_degree as number,\n      outDegree: row.out_degree as number,\n    }));\n  }\n\n  /**\n   * Find surprising cross-file connections: direct edges between nodes in\n   * structurally distant files. Scored by path distance \u00D7 edge-kind weight.\n   */\n  findSurprisingConnections(limit = 20): Array<{ source: Node; target: Node; kind: string; score: number }> {\n    const KIND_WEIGHT: Record<string, number> = {\n      calls: 1.0, references: 0.8, type_of: 0.7, returns: 0.6,\n      decorates: 0.6, extends: 0.5, implements: 0.5,\n    };\n\n    const rows: Array<{ source: string; target: string; kind: string; source_file: string; target_file: string }> =\n      this.db.all(\n        `SELECT e.source, e.target, e.kind,\n                ns.file_path AS source_file, nt.file_path AS target_file\n         FROM edges e\n         JOIN nodes ns ON ns.id = e.source\n         JOIN nodes nt ON nt.id = e.target\n         WHERE ns.file_path != nt.file_path\n           AND e.kind NOT IN ('contains', 'import', 'imports')\n         LIMIT 5000`\n      );\n\n    // Score: path distance \u00D7 kind weight\n    const scored = rows.map(row => {\n      const srcDirs = row.source_file.split('/').slice(0, -1);\n      const tgtDirs = row.target_file.split('/').slice(0, -1);\n      let common = 0;\n      for (let i = 0; i < Math.min(srcDirs.length, tgtDirs.length); i++) {\n        if (srcDirs[i] === tgtDirs[i]) common++;\n        else break;\n      }\n      const maxDirs = Math.max(srcDirs.length, tgtDirs.length, 1);\n      const pathSimilarity = common / maxDirs;\n      const kindWeight = KIND_WEIGHT[row.kind] ?? 0.4;\n      return { ...row, score: (1 - pathSimilarity) * kindWeight };\n    });\n\n    // Sort desc, deduplicate by source+target+kind\n    scored.sort((a, b) => b.score - a.score);\n    const seen = new Set<string>();\n    const top: typeof scored = [];\n    for (const row of scored) {\n      const key = `${row.source}|${row.target}|${row.kind}`;\n      if (!seen.has(key)) {\n        seen.add(key);\n        top.push(row);\n        if (top.length >= limit) break;\n      }\n    }\n\n    const result: Array<{ source: Node; target: Node; kind: string; score: number }> = [];\n    for (const row of top) {\n      const src = this.getNode(row.source);\n      const tgt = this.getNode(row.target);\n      if (src && tgt) result.push({ source: src, target: tgt, kind: row.kind, score: row.score });\n    }\n    return result;\n  }\n\n  getStats(): GraphStats {\n    const files = this.db.get('SELECT COUNT(*) as c FROM files').c;\n    const nodes = this.db.get('SELECT COUNT(*) as c FROM nodes').c;\n    const edges = this.db.get('SELECT COUNT(*) as c FROM edges').c;\n    const kindRows = this.db.all('SELECT kind, COUNT(*) as c FROM nodes GROUP BY kind');\n    const nodesByKind: Record<string, number> = {};\n    for (const row of kindRows) nodesByKind[row.kind] = row.c;\n    const langRows = this.db.all('SELECT language, COUNT(*) as c FROM files GROUP BY language');\n    const filesByLanguage: Record<string, number> = {};\n    for (const row of langRows) filesByLanguage[row.language] = row.c;\n    const dbPath = path.join(this.projectRoot, '.kirograph', 'kirograph.db');\n    let dbSizeBytes = 0;\n    try { dbSizeBytes = fs.statSync(dbPath).size; } catch { /* ignore */ }\n    const embeddingCount = this.getEmbeddingCount();\n    return { files, nodes, edges, nodesByKind, filesByLanguage, dbSizeBytes, embeddingCount, embeddingsEnabled: false, embeddingModel: '', useVecIndex: false, semanticEngine: 'cosine' as const, vecIndexCount: 0, engineFallback: null, embeddableNodeCount: 0, frameworks: [], architectureEnabled: false };\n  }\n\n  // \u2500\u2500 Architecture \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  clearArchitecture(): void {\n    this.db.run('DELETE FROM arch_coupling');\n    this.db.run('DELETE FROM arch_layer_deps');\n    this.db.run('DELETE FROM arch_package_deps');\n    this.db.run('DELETE FROM arch_file_layers');\n    this.db.run('DELETE FROM arch_file_packages');\n    this.db.run('DELETE FROM arch_layers');\n    this.db.run('DELETE FROM arch_packages');\n  }\n\n  upsertArchPackage(pkg: ArchPackage): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_packages\n        (id, name, path, source, language, manifest_path, version, external_deps, metadata, updated_at)\n       VALUES (?,?,?,?,?,?,?,?,?,?)`,\n      [\n        pkg.id, pkg.name, pkg.path, pkg.source,\n        pkg.language ?? null, pkg.manifestPath ?? null, pkg.version ?? null,\n        pkg.externalDeps ? JSON.stringify(pkg.externalDeps) : null,\n        pkg.metadata ? JSON.stringify(pkg.metadata) : null,\n        pkg.updatedAt,\n      ]\n    );\n  }\n\n  upsertArchLayer(layer: ArchLayer): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_layers (id, name, source, patterns, metadata, updated_at)\n       VALUES (?,?,?,?,?,?)`,\n      [\n        layer.id, layer.name, layer.source,\n        JSON.stringify(layer.patterns),\n        layer.metadata ? JSON.stringify(layer.metadata) : null,\n        layer.updatedAt,\n      ]\n    );\n  }\n\n  upsertArchFilePackage(filePath: string, packageId: string): void {\n    this.db.run(\n      'INSERT OR IGNORE INTO arch_file_packages (file_path, package_id) VALUES (?,?)',\n      [filePath, packageId]\n    );\n  }\n\n  upsertArchFileLayer(filePath: string, layerId: string, confidence: number, matchedPattern: string): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence, matched_pattern)\n       VALUES (?,?,?,?)`,\n      [filePath, layerId, confidence, matchedPattern]\n    );\n  }\n\n  upsertArchPackageDep(sourcePkg: string, targetPkg: string, depCount: number, files?: Array<{ from: string; to: string }>): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_package_deps (source_pkg, target_pkg, dep_count, files)\n       VALUES (?,?,?,?)`,\n      [sourcePkg, targetPkg, depCount, files ? JSON.stringify(files) : null]\n    );\n  }\n\n  upsertArchLayerDep(sourceLayer: string, targetLayer: string, depCount: number): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_layer_deps (source_layer, target_layer, dep_count)\n       VALUES (?,?,?)`,\n      [sourceLayer, targetLayer, depCount]\n    );\n  }\n\n  upsertArchCoupling(coupling: ArchCoupling): void {\n    this.db.run(\n      `INSERT OR REPLACE INTO arch_coupling (package_id, afferent, efferent, instability, updated_at)\n       VALUES (?,?,?,?,?)`,\n      [coupling.packageId, coupling.afferent, coupling.efferent, coupling.instability, coupling.updatedAt]\n    );\n  }\n\n  getArchPackages(): ArchPackage[] {\n    return this.db.all('SELECT * FROM arch_packages').map((r: any): ArchPackage => ({\n      id: r.id,\n      name: r.name,\n      path: r.path,\n      source: r.source,\n      language: r.language ?? undefined,\n      manifestPath: r.manifest_path ?? undefined,\n      version: r.version ?? undefined,\n      externalDeps: r.external_deps ? JSON.parse(r.external_deps) : undefined,\n      metadata: r.metadata ? JSON.parse(r.metadata) : undefined,\n      updatedAt: r.updated_at,\n    }));\n  }\n\n  getArchLayers(): ArchLayer[] {\n    return this.db.all('SELECT * FROM arch_layers').map((r: any): ArchLayer => ({\n      id: r.id,\n      name: r.name,\n      source: r.source,\n      patterns: JSON.parse(r.patterns),\n      metadata: r.metadata ? JSON.parse(r.metadata) : undefined,\n      updatedAt: r.updated_at,\n    }));\n  }\n\n  getArchPackageDeps(): ArchPackageDep[] {\n    return this.db.all('SELECT * FROM arch_package_deps').map((r: any): ArchPackageDep => ({\n      sourcePkg: r.source_pkg,\n      targetPkg: r.target_pkg,\n      depCount: r.dep_count,\n      files: r.files ? JSON.parse(r.files) : undefined,\n    }));\n  }\n\n  getArchLayerDeps(): ArchLayerDep[] {\n    return this.db.all('SELECT * FROM arch_layer_deps').map((r: any): ArchLayerDep => ({\n      sourceLayer: r.source_layer,\n      targetLayer: r.target_layer,\n      depCount: r.dep_count,\n    }));\n  }\n\n  getArchCoupling(): ArchCoupling[] {\n    return this.db.all('SELECT * FROM arch_coupling').map((r: any): ArchCoupling => ({\n      packageId: r.package_id,\n      afferent: r.afferent,\n      efferent: r.efferent,\n      instability: r.instability,\n      updatedAt: r.updated_at,\n    }));\n  }\n\n  getArchStats(): { packages: number; layers: number; packageDeps: number } {\n    return {\n      packages: this.db.get('SELECT COUNT(*) as c FROM arch_packages')?.c ?? 0,\n      layers: this.db.get('SELECT COUNT(*) as c FROM arch_layers')?.c ?? 0,\n      packageDeps: this.db.get('SELECT COUNT(*) as c FROM arch_package_deps')?.c ?? 0,\n    };\n  }\n\n  /**\n   * Return file-to-file import relationships by joining edges + nodes.\n   * Used by ArchitectureAnalyzer to roll up package-level dependencies.\n   */\n  getFileImportPairs(): Array<{ sourceFile: string; targetFile: string }> {\n    return this.db.all(\n      `SELECT DISTINCT n1.file_path as source_file, n2.file_path as target_file\n       FROM edges e\n       JOIN nodes n1 ON n1.id = e.source\n       JOIN nodes n2 ON n2.id = e.target\n       WHERE e.kind = 'imports' AND n1.file_path != n2.file_path`\n    ).map((r: any) => ({ sourceFile: r.source_file, targetFile: r.target_file }));\n  }\n\n  getArchFilePackages(): Array<{ filePath: string; packageId: string }> {\n    return this.db.all('SELECT file_path, package_id FROM arch_file_packages')\n      .map((r: any) => ({ filePath: r.file_path, packageId: r.package_id }));\n  }\n\n  getArchFileLayers(): Array<{ filePath: string; layerId: string; confidence: number; matchedPattern: string }> {\n    return this.db.all('SELECT file_path, layer_id, confidence, matched_pattern FROM arch_file_layers')\n      .map((r: any) => ({\n        filePath: r.file_path,\n        layerId: r.layer_id,\n        confidence: r.confidence,\n        matchedPattern: r.matched_pattern,\n      }));\n  }\n\n  getArchitectureResult(): {\n    packages: ArchPackage[];\n    layers: ArchLayer[];\n    packageDeps: ArchPackageDep[];\n    layerDeps: ArchLayerDep[];\n    coupling: ArchCoupling[];\n  } {\n    return {\n      packages: this.getArchPackages(),\n      layers: this.getArchLayers(),\n      packageDeps: this.getArchPackageDeps(),\n      layerDeps: this.getArchLayerDeps(),\n      coupling: this.getArchCoupling(),\n    };\n  }\n\n  // \u2500\u2500 Transactions \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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  transaction<T>(fn: () => T): T {\n    this.db.run('BEGIN');\n    try {\n      const result = fn();\n      this.db.run('COMMIT');\n      return result;\n    } catch (err) {\n      this.db.run('ROLLBACK');\n      throw err;\n    }\n  }\n\n  close(): void {\n    this.db.close();\n  }\n}\n"],
+  "mappings": 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   "names": ["placeholders"]
 }

package/dist/db/memory-schema.sql

@@ -24,13 +24,17 @@ CREATE TABLE IF NOT EXISTS mem_observations (
   valid_from INTEGER,
   valid_until INTEGER,
   superseded_by TEXT,
-  fact_type TEXT DEFAULT 'observation'
+  fact_type TEXT DEFAULT 'observation',
+  topic_key TEXT,
+  review_after INTEGER
 );
 
 CREATE UNIQUE INDEX IF NOT EXISTS idx_mem_obs_hash ON mem_observations(content_hash);
 CREATE INDEX IF NOT EXISTS idx_mem_obs_session ON mem_observations(session_id);
 CREATE INDEX IF NOT EXISTS idx_mem_obs_kind ON mem_observations(kind);
 CREATE INDEX IF NOT EXISTS idx_mem_obs_created ON mem_observations(created_at);
+CREATE INDEX IF NOT EXISTS idx_mem_obs_topic ON mem_observations(topic_key);
+CREATE INDEX IF NOT EXISTS idx_mem_obs_review ON mem_observations(review_after);
 
 CREATE VIRTUAL TABLE IF NOT EXISTS mem_fts USING fts5(
   id UNINDEXED,
@@ -53,3 +57,32 @@ CREATE TABLE IF NOT EXISTS mem_vectors (
   model TEXT NOT NULL,
   created_at INTEGER NOT NULL
 );
+
+-- Relations between observations (conflict detection)
+CREATE TABLE IF NOT EXISTS mem_relations (
+  id TEXT PRIMARY KEY,
+  observation_a TEXT NOT NULL REFERENCES mem_observations(id) ON DELETE CASCADE,
+  observation_b TEXT NOT NULL REFERENCES mem_observations(id) ON DELETE CASCADE,
+  relation TEXT NOT NULL,
+  confidence REAL NOT NULL DEFAULT 1.0,
+  reason TEXT,
+  evidence TEXT,
+  judgment_status TEXT NOT NULL DEFAULT 'pending',
+  judged_at INTEGER,
+  created_at INTEGER NOT NULL,
+  UNIQUE(observation_a, observation_b)
+);
+
+CREATE INDEX IF NOT EXISTS idx_mem_rel_a ON mem_relations(observation_a);
+CREATE INDEX IF NOT EXISTS idx_mem_rel_b ON mem_relations(observation_b);
+CREATE INDEX IF NOT EXISTS idx_mem_rel_status ON mem_relations(judgment_status);
+
+-- Saved prompts linked to sessions
+CREATE TABLE IF NOT EXISTS mem_prompts (
+  id TEXT PRIMARY KEY,
+  session_id TEXT REFERENCES mem_sessions(id) ON DELETE CASCADE,
+  content TEXT NOT NULL,
+  created_at INTEGER NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_mem_prompts_session ON mem_prompts(session_id);

package/dist/db/wiki-schema.sql

@@ -0,0 +1,40 @@
+-- KiroGraph Wiki Schema (opt-in, enableWiki=true)
+-- Isolated from core graph tables. Source of truth is .kirograph/wiki/*.md files.
+-- This is a fast-search index; regeneratable via `kirograph wiki reindex`.
+
+CREATE TABLE IF NOT EXISTS wiki_pages (
+  slug        TEXT PRIMARY KEY,   -- e.g. "AuthService", "arch/auth-model"
+  title       TEXT NOT NULL,
+  content     TEXT NOT NULL,      -- full markdown content
+  file_path   TEXT,               -- relative path under .kirograph/wiki/ (null if not yet written)
+  updated_at  INTEGER NOT NULL,   -- epoch ms of last ingest
+  source_count INTEGER DEFAULT 0  -- number of sources that contributed to this page
+);
+
+-- Standalone FTS5 table (stores its own copy of indexed content)
+CREATE VIRTUAL TABLE IF NOT EXISTS wiki_fts
+  USING fts5(slug, title, content, tokenize='porter ascii');
+
+-- Keep FTS in sync (insert)
+CREATE TRIGGER IF NOT EXISTS wiki_fts_insert AFTER INSERT ON wiki_pages BEGIN
+  INSERT INTO wiki_fts(rowid, slug, title, content) VALUES (new.rowid, new.slug, new.title, new.content);
+END;
+
+-- Keep FTS in sync (update: delete old FTS entry then insert new)
+CREATE TRIGGER IF NOT EXISTS wiki_fts_update AFTER UPDATE ON wiki_pages BEGIN
+  DELETE FROM wiki_fts WHERE rowid = old.rowid;
+  INSERT INTO wiki_fts(rowid, slug, title, content) VALUES (new.rowid, new.slug, new.title, new.content);
+END;
+
+-- Keep FTS in sync (delete)
+CREATE TRIGGER IF NOT EXISTS wiki_fts_delete AFTER DELETE ON wiki_pages BEGIN
+  DELETE FROM wiki_fts WHERE rowid = old.rowid;
+END;
+
+-- Pending sources for local-model synthesis (wikiSynthesisMode: 'local')
+CREATE TABLE IF NOT EXISTS wiki_queue (
+  id          INTEGER PRIMARY KEY AUTOINCREMENT,
+  source_name TEXT NOT NULL,
+  source_text TEXT NOT NULL,
+  queued_at   INTEGER NOT NULL
+);

package/dist/mcp/server.js

@@ -35,6 +35,7 @@ var path = __toESM(require("path"));
 var import__ = __toESM(require("../index"));
 var import_transport = require("./transport");
 var import_tools = require("./tools");
+var import_tool_names = require("./tool-names");
 var import_runner = require("../patterns/runner");
 const SERVER_INFO = { name: "kirograph", version: "0.1.0" };
 const PROTOCOL_VERSION = "2024-11-05";
@@ -44,10 +45,14 @@ class MCPServer {
     this.cg = null;
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     this.config = null;
+    this.enabledTools = [];
+    this.enabledToolNames = /* @__PURE__ */ new Set();
     this.projectPath = projectPath ? path.resolve(projectPath) : null;
     this.toolHandler = new import_tools.ToolHandler(null);
+    this.setEnabledTools();
   }
   async start() {
+    if (this.projectPath) await this.tryInit(this.projectPath);
     this.transport.start(this.handleMessage.bind(this));
     process.on("SIGINT", () => this.stop());
     process.on("SIGTERM", () => this.stop());
@@ -73,17 +78,18 @@ class MCPServer {
       this.config = await loadConfig(root);
     } catch {
     }
+    this.setEnabledTools();
   }
   async handleMessage(msg) {
     const req = msg;
     switch (req.method) {
       case "initialize": {
-        const rootUri = req.params?.rootUri ?? req.params?.workspaceFolders?.[0]?.uri;
-        if (rootUri) {
-          const p = rootUri.startsWith("file://") ? decodeURIComponent(rootUri.replace(/^file:\/\/\/?/, "")) : rootUri;
-          await this.tryInit(p);
-        } else if (this.projectPath) {
-          await this.tryInit(this.projectPath);
+        if (!this.config) {
+          const rootUri = req.params?.rootUri ?? req.params?.workspaceFolders?.[0]?.uri;
+          if (rootUri) {
+            const p = rootUri.startsWith("file://") ? decodeURIComponent(rootUri.replace(/^file:\/\/\/?/, "")) : rootUri;
+            await this.tryInit(p);
+          }
         }
         return {
           protocolVersion: PROTOCOL_VERSION,
@@ -92,14 +98,16 @@ class MCPServer {
         };
       }
       case "tools/list": {
-        const dynamicTools = [...import_tools.tools];
-        if (this.config?.enablePatterns && new import_runner.PatternRunner().isAvailable()) {
-          dynamicTools.push(import_tools.LIVE_SEARCH_TOOL_DEFINITION);
-        }
-        return { tools: dynamicTools };
+        return { tools: this.enabledTools };
       }
       case "tools/call": {
         const { name, arguments: args = {} } = req.params ?? {};
+        if (!this.enabledToolNames.has(name)) {
+          return {
+            content: [{ type: "text", text: `Tool "${name}" is not available. The feature it belongs to is not enabled in .kirograph/config.json.` }],
+            isError: true
+          };
+        }
         try {
           return await this.toolHandler.handle(name, args);
         } catch (err) {
@@ -117,6 +125,22 @@ class MCPServer {
         return void 0;
     }
   }
+  setEnabledTools() {
+    const hidden = /* @__PURE__ */ new Set();
+    if (this.config) {
+      for (const [flag, names] of Object.entries(import_tool_names.FEATURE_TOOL_SETS)) {
+        if (this.config[flag] === false) {
+          for (const n of names) hidden.add(n);
+        }
+      }
+    }
+    const list = import_tools.tools.filter((t) => !hidden.has(t.name));
+    if (this.config?.enablePatterns && new import_runner.PatternRunner().isAvailable()) {
+      list.push(import_tools.LIVE_SEARCH_TOOL_DEFINITION);
+    }
+    this.enabledTools = list;
+    this.enabledToolNames = new Set(list.map((t) => t.name));
+  }
   stop() {
     this.cg?.close();
     this.toolHandler.closeAll();

package/dist/mcp/server.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/mcp/server.ts"],
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