ctxo-mcp 0.4.0 → 0.4.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ctxo-mcp",
-  "version": "0.4.0",
+  "version": "0.4.2",
   "description": "MCP server delivering dependency-aware, history-enriched context for codebases",
   "type": "module",
   "engines": {

package/dist/chunk-BMB6SQIR.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/core/logger.ts","../src/adapters/storage/sqlite-storage-adapter.ts","../src/adapters/git/simple-git-adapter.ts","../src/core/why-context/revert-detector.ts","../src/core/co-change/co-change-analyzer.ts"],"sourcesContent":["/**\n * Structured logger for Ctxo — all output goes to stderr (stdout reserved for MCP JSON-RPC).\n *\n * Supports debug mode via DEBUG environment variable:\n *   DEBUG=ctxo:*          — all debug output\n *   DEBUG=ctxo:git        — only git adapter debug\n *   DEBUG=ctxo:index      — only indexing debug\n *   DEBUG=ctxo:mcp        — only MCP handler debug\n *   DEBUG=ctxo:storage    — only storage adapter debug\n *   DEBUG=ctxo:masking    — only masking pipeline debug\n *\n * Always outputs: info, warn, error (regardless of DEBUG).\n * Only outputs debug when matching namespace is enabled.\n */\n\nfunction isDebugEnabled(namespace: string): boolean {\n  const debugEnv = process.env['DEBUG'] ?? '';\n  if (!debugEnv) return false;\n  const patterns = debugEnv.split(',').map(p => p.trim());\n  return patterns.some(p => {\n    if (p === '*' || p === 'ctxo:*') return true;\n    if (p === namespace) return true;\n    if (p.endsWith(':*') && namespace.startsWith(p.slice(0, -1))) return true;\n    return false;\n  });\n}\n\nexport interface Logger {\n  debug(message: string, ...args: unknown[]): void;\n  info(message: string, ...args: unknown[]): void;\n  warn(message: string, ...args: unknown[]): void;\n  error(message: string, ...args: unknown[]): void;\n}\n\nexport function createLogger(namespace: string): Logger {\n  const prefix = `[${namespace}]`;\n\n  return {\n    debug(message: string, ...args: unknown[]) {\n      if (isDebugEnabled(namespace)) {\n        console.error(`${prefix} DEBUG ${message}`, ...args);\n      }\n    },\n    info(message: string, ...args: unknown[]) {\n      console.error(`${prefix} ${message}`, ...args);\n    },\n    warn(message: string, ...args: unknown[]) {\n      console.error(`${prefix} WARN ${message}`, ...args);\n    },\n    error(message: string, ...args: unknown[]) {\n      console.error(`${prefix} ERROR ${message}`, ...args);\n    },\n  };\n}\n","import initSqlJs, { type Database } from 'sql.js';\nimport { readFileSync, writeFileSync, existsSync, mkdirSync } from 'node:fs';\nimport { join, dirname } from 'node:path';\nimport type { FileIndex, GraphEdge, SymbolNode } from '../../core/types.js';\nimport type { IStoragePort } from '../../ports/i-storage-port.js';\nimport { JsonIndexReader } from './json-index-reader.js';\nimport { createLogger } from '../../core/logger.js';\n\nconst log = createLogger('ctxo:storage');\n\nexport class SqliteStorageAdapter implements IStoragePort {\n  private db: Database | undefined;\n  private readonly dbPath: string;\n  private readonly ctxoRoot: string;\n\n  constructor(ctxoRoot: string) {\n    this.ctxoRoot = ctxoRoot;\n    this.dbPath = join(ctxoRoot, '.cache', 'symbols.db');\n  }\n\n  async init(): Promise<void> {\n    const SQL = await initSqlJs();\n\n    if (existsSync(this.dbPath)) {\n      try {\n        const buffer = readFileSync(this.dbPath);\n        this.db = new SQL.Database(buffer);\n        this.verifyIntegrity();\n      } catch {\n        log.warn('Corrupt DB detected, rebuilding from JSON index');\n        this.db = new SQL.Database();\n        this.createTables();\n      }\n    } else {\n      this.db = new SQL.Database();\n      this.createTables();\n    }\n\n    // Always rebuild from JSON — it is the source of truth\n    this.rebuildFromJson();\n  }\n\n  async initEmpty(): Promise<void> {\n    const SQL = await initSqlJs();\n    this.db = new SQL.Database();\n    this.createTables();\n  }\n\n  private database(): Database {\n    if (!this.db) {\n      throw new Error('SqliteStorageAdapter not initialized. Call init() first.');\n    }\n    return this.db;\n  }\n\n  private verifyIntegrity(): void {\n    const db = this.database();\n    const result = db.exec('PRAGMA integrity_check');\n    const firstRow = result[0]?.values[0];\n    if (!firstRow || firstRow[0] !== 'ok') {\n      throw new Error('SQLite integrity check failed');\n    }\n\n    const tables = db.exec(\n      \"SELECT name FROM sqlite_master WHERE type='table' AND name IN ('symbols', 'edges', 'files')\",\n    );\n    if (!tables[0] || tables[0].values.length < 3) {\n      throw new Error('Missing required tables');\n    }\n  }\n\n  private createTables(): void {\n    const db = this.database();\n    db.run(`\n      CREATE TABLE IF NOT EXISTS files (\n        file_path TEXT PRIMARY KEY,\n        last_modified INTEGER NOT NULL\n      )\n    `);\n    db.run(`\n      CREATE TABLE IF NOT EXISTS symbols (\n        symbol_id TEXT PRIMARY KEY,\n        name TEXT NOT NULL,\n        kind TEXT NOT NULL,\n        file_path TEXT NOT NULL,\n        start_line INTEGER NOT NULL,\n        end_line INTEGER NOT NULL\n      )\n    `);\n    db.run(`\n      CREATE TABLE IF NOT EXISTS edges (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        from_symbol TEXT NOT NULL,\n        to_symbol TEXT NOT NULL,\n        kind TEXT NOT NULL\n      )\n    `);\n    db.run('CREATE INDEX IF NOT EXISTS idx_symbols_file ON symbols(file_path)');\n    db.run('CREATE INDEX IF NOT EXISTS idx_edges_from ON edges(from_symbol)');\n    db.run('CREATE INDEX IF NOT EXISTS idx_edges_to ON edges(to_symbol)');\n  }\n\n  private rebuildFromJson(): void {\n    const reader = new JsonIndexReader(this.ctxoRoot);\n    const indices = reader.readAll();\n\n    if (indices.length > 0) {\n      this.bulkWrite(indices);\n    }\n  }\n\n  writeSymbolFile(fileIndex: FileIndex): void {\n    const db = this.database();\n\n    db.run('BEGIN TRANSACTION');\n    try {\n      this.deleteFileData(db, fileIndex.file);\n\n      db.run(\n        'INSERT INTO files (file_path, last_modified) VALUES (?, ?)',\n        [fileIndex.file, fileIndex.lastModified],\n      );\n\n      for (const sym of fileIndex.symbols) {\n        db.run(\n          'INSERT OR REPLACE INTO symbols (symbol_id, name, kind, file_path, start_line, end_line) VALUES (?, ?, ?, ?, ?, ?)',\n          [sym.symbolId, sym.name, sym.kind, fileIndex.file, sym.startLine, sym.endLine],\n        );\n      }\n\n      for (const edge of fileIndex.edges) {\n        db.run(\n          'INSERT INTO edges (from_symbol, to_symbol, kind) VALUES (?, ?, ?)',\n          [edge.from, edge.to, edge.kind],\n        );\n      }\n\n      db.run('COMMIT');\n      this.persistIfNeeded();\n    } catch (err) {\n      db.run('ROLLBACK');\n      throw err;\n    }\n  }\n\n  /**\n   * Read symbol file from SQLite cache.\n   * NOTE: SQLite only caches symbols + edges (graph topology).\n   * intent, antiPatterns, and complexity live in committed JSON index only.\n   * Use JsonIndexReader for full FileIndex data.\n   */\n  readSymbolFile(relativePath: string): FileIndex | undefined {\n    const db = this.database();\n\n    const fileResult = db.exec(\n      'SELECT file_path, last_modified FROM files WHERE file_path = ?',\n      [relativePath],\n    );\n    if (!fileResult[0] || fileResult[0].values.length === 0) {\n      return undefined;\n    }\n\n    const [filePath, lastModified] = fileResult[0].values[0] as [string, number];\n\n    const symbols = this.getSymbolsForFile(db, filePath);\n    const edges = this.getEdgesForFile(db, filePath);\n\n    return {\n      file: filePath,\n      lastModified,\n      symbols,\n      edges,\n      // Not stored in SQLite — use JsonIndexReader for these fields\n      intent: [],\n      antiPatterns: [],\n    };\n  }\n\n  listIndexedFiles(): string[] {\n    const db = this.database();\n    const result = db.exec('SELECT file_path FROM files ORDER BY file_path');\n    if (!result[0]) return [];\n    return result[0].values.map((row) => row[0] as string);\n  }\n\n  deleteSymbolFile(relativePath: string): void {\n    const db = this.database();\n    this.deleteFileData(db, relativePath);\n  }\n\n  getSymbolById(symbolId: string): SymbolNode | undefined {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT symbol_id, name, kind, start_line, end_line FROM symbols WHERE symbol_id = ?',\n      [symbolId],\n    );\n    if (!result[0] || result[0].values.length === 0) {\n      return undefined;\n    }\n\n    const [sid, name, kind, startLine, endLine] = result[0].values[0] as [string, string, string, number, number];\n    return { symbolId: sid, name, kind: kind as SymbolNode['kind'], startLine, endLine };\n  }\n\n  getEdgesFrom(symbolId: string): GraphEdge[] {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT from_symbol, to_symbol, kind FROM edges WHERE from_symbol = ?',\n      [symbolId],\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      from: row[0] as string,\n      to: row[1] as string,\n      kind: row[2] as GraphEdge['kind'],\n    }));\n  }\n\n  getEdgesTo(symbolId: string): GraphEdge[] {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT from_symbol, to_symbol, kind FROM edges WHERE to_symbol = ?',\n      [symbolId],\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      from: row[0] as string,\n      to: row[1] as string,\n      kind: row[2] as GraphEdge['kind'],\n    }));\n  }\n\n  getAllSymbols(): SymbolNode[] {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT symbol_id, name, kind, start_line, end_line FROM symbols',\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      symbolId: row[0] as string,\n      name: row[1] as string,\n      kind: row[2] as SymbolNode['kind'],\n      startLine: row[3] as number,\n      endLine: row[4] as number,\n    }));\n  }\n\n  getAllEdges(): GraphEdge[] {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT from_symbol, to_symbol, kind FROM edges',\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      from: row[0] as string,\n      to: row[1] as string,\n      kind: row[2] as GraphEdge['kind'],\n    }));\n  }\n\n  bulkWrite(indices: FileIndex[]): void {\n    const db = this.database();\n\n    db.run('BEGIN TRANSACTION');\n    try {\n      for (const fileIndex of indices) {\n        this.deleteFileData(db, fileIndex.file);\n\n        db.run(\n          'INSERT INTO files (file_path, last_modified) VALUES (?, ?)',\n          [fileIndex.file, fileIndex.lastModified],\n        );\n\n        for (const sym of fileIndex.symbols) {\n          db.run(\n            'INSERT OR REPLACE INTO symbols (symbol_id, name, kind, file_path, start_line, end_line) VALUES (?, ?, ?, ?, ?, ?)',\n            [sym.symbolId, sym.name, sym.kind, fileIndex.file, sym.startLine, sym.endLine],\n          );\n        }\n\n        for (const edge of fileIndex.edges) {\n          db.run(\n            'INSERT INTO edges (from_symbol, to_symbol, kind) VALUES (?, ?, ?)',\n            [edge.from, edge.to, edge.kind],\n          );\n        }\n      }\n\n      db.run('COMMIT');\n      this.persistIfNeeded();\n    } catch (err) {\n      db.run('ROLLBACK');\n      throw err;\n    }\n  }\n\n  persist(): void {\n    const db = this.database();\n    const data = db.export();\n    const buffer = Buffer.from(data);\n    mkdirSync(dirname(this.dbPath), { recursive: true });\n    writeFileSync(this.dbPath, buffer);\n  }\n\n  close(): void {\n    if (this.db) {\n      this.persist();\n      this.db.close();\n      this.db = undefined;\n    }\n  }\n\n  private persistIfNeeded(): void {\n    try {\n      this.persist();\n    } catch (err) {\n      log.error(`Failed to persist DB: ${(err as Error).message}`);\n    }\n  }\n\n  private deleteFileData(db: Database, filePath: string): void {\n    // Delete edges originating from this file's symbols\n    const symResult = db.exec(\n      'SELECT symbol_id FROM symbols WHERE file_path = ?',\n      [filePath],\n    );\n    if (symResult[0]) {\n      for (const row of symResult[0].values) {\n        db.run('DELETE FROM edges WHERE from_symbol = ?', [row[0]]);\n      }\n    }\n    db.run('DELETE FROM symbols WHERE file_path = ?', [filePath]);\n    db.run('DELETE FROM files WHERE file_path = ?', [filePath]);\n  }\n\n  private getSymbolsForFile(db: Database, filePath: string): SymbolNode[] {\n    const result = db.exec(\n      'SELECT symbol_id, name, kind, start_line, end_line FROM symbols WHERE file_path = ? ORDER BY start_line',\n      [filePath],\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      symbolId: row[0] as string,\n      name: row[1] as string,\n      kind: row[2] as SymbolNode['kind'],\n      startLine: row[3] as number,\n      endLine: row[4] as number,\n    }));\n  }\n\n  private getEdgesForFile(db: Database, filePath: string): GraphEdge[] {\n    const result = db.exec(\n      `SELECT e.from_symbol, e.to_symbol, e.kind FROM edges e\n       INNER JOIN symbols s ON e.from_symbol = s.symbol_id\n       WHERE s.file_path = ?`,\n      [filePath],\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      from: row[0] as string,\n      to: row[1] as string,\n      kind: row[2] as GraphEdge['kind'],\n    }));\n  }\n}\n","import { simpleGit, type SimpleGit } from 'simple-git';\nimport type { IGitPort } from '../../ports/i-git-port.js';\nimport type { CommitRecord, ChurnData } from '../../core/types.js';\nimport { createLogger } from '../../core/logger.js';\n\nconst log = createLogger('ctxo:git');\n\nexport class SimpleGitAdapter implements IGitPort {\n  private readonly git: SimpleGit;\n\n  constructor(projectRoot: string) {\n    this.git = simpleGit(projectRoot);\n    log.debug('Initialized with root: %s', projectRoot);\n  }\n\n  async isAvailable(): Promise<boolean> {\n    try {\n      await this.git.version();\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  async getCommitHistory(filePath: string, maxCount?: number): Promise<CommitRecord[]> {\n    try {\n      const log = await this.git.log({\n        file: filePath,\n        '--follow': null,\n        ...(maxCount ? { maxCount } : {}),\n      });\n\n      return log.all.map((entry) => ({\n        hash: entry.hash,\n        message: entry.message,\n        date: entry.date,\n        author: entry.author_name,\n      }));\n    } catch (err) {\n      log.error(` Failed to get history for ${filePath}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  async getBatchHistory(maxCount = 20): Promise<Map<string, CommitRecord[]>> {\n    try {\n      const log = await this.git.log({ maxCount: maxCount * 50, '--name-only': null });\n      const result = new Map<string, CommitRecord[]>();\n\n      for (const entry of log.all) {\n        const record: CommitRecord = {\n          hash: entry.hash,\n          message: entry.message,\n          date: entry.date,\n          author: entry.author_name,\n        };\n\n        const diff = entry.diff;\n        const files: string[] = diff?.files?.map((f: { file: string }) => f.file.replace(/\\\\/g, '/')) ?? [];\n\n        for (const file of files) {\n          let list = result.get(file);\n          if (!list) { list = []; result.set(file, list); }\n          if (list.length < maxCount) {\n            list.push(record);\n          }\n        }\n      }\n\n      return result;\n    } catch (err) {\n      log.error(` Batch history failed: ${(err as Error).message}`);\n      return new Map();\n    }\n  }\n\n  async getChangedFiles(since: string): Promise<string[]> {\n    try {\n      const diff = await this.git.diffSummary([since]);\n      return diff.files.map((f) => f.file.replace(/\\\\/g, '/'));\n    } catch (err) {\n      log.error(` Failed to get changed files since ${since}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  async getFileChurn(filePath: string): Promise<ChurnData> {\n    try {\n      const log = await this.git.log({ file: filePath, '--follow': null });\n\n      return {\n        filePath,\n        commitCount: log.total,\n      };\n    } catch (err) {\n      log.error(` Failed to get churn for ${filePath}: ${(err as Error).message}`);\n      return { filePath, commitCount: 0 };\n    }\n  }\n}\n","import type { CommitRecord, AntiPattern } from '../types.js';\n\n// Explicit revert patterns\nconst REVERT_QUOTED_PATTERN = /^Revert \"(.+)\"$/;\nconst REVERT_PREFIX_PATTERN = /^revert:\\s*(.+)$/i;\n\n// Undo/rollback patterns\nconst UNDO_PATTERN = /^undo[:\\s]/i;\nconst ROLLBACK_PATTERN = /^rollback[:\\s]/i;\n\n// Indirect revert indicators (keywords in commit message body)\nconst INDIRECT_KEYWORDS = [\n  /\\brevert(?:s|ed|ing)?\\b/i,\n  /\\broll(?:s|ed|ing)?\\s*back\\b/i,\n  /\\bundo(?:es|ne|ing)?\\b/i,\n  /\\bbacked?\\s*out\\b/i,\n  /\\bremov(?:e|es|ed|ing)\\s+(?:broken|buggy|faulty)\\b/i,\n];\n\nexport class RevertDetector {\n  detect(commits: readonly CommitRecord[]): AntiPattern[] {\n    const antiPatterns: AntiPattern[] = [];\n\n    for (const commit of commits) {\n      if (!commit.message) continue;\n\n      if (this.isRevert(commit.message)) {\n        antiPatterns.push({\n          hash: commit.hash,\n          message: commit.message,\n          date: commit.date,\n        });\n      }\n    }\n\n    return antiPatterns;\n  }\n\n  private isRevert(message: string): boolean {\n    // Explicit patterns (high confidence)\n    if (REVERT_QUOTED_PATTERN.test(message)) return true;\n    if (REVERT_PREFIX_PATTERN.test(message)) return true;\n    if (UNDO_PATTERN.test(message)) return true;\n    if (ROLLBACK_PATTERN.test(message)) return true;\n\n    // Indirect indicators (keyword search in full message)\n    for (const pattern of INDIRECT_KEYWORDS) {\n      if (pattern.test(message)) return true;\n    }\n\n    return false;\n  }\n}\n","import type { CoChangeEntry, CoChangeMatrix, FileIndex } from '../types.js';\n\nconst MIN_SHARED_COMMITS = 2;\nconst MIN_FREQUENCY = 0.1;\n\nexport function aggregateCoChanges(indices: readonly FileIndex[]): CoChangeMatrix {\n  // Step 1: Build commit → files map\n  const commitToFiles = new Map<string, Set<string>>();\n  const fileCommitCounts = new Map<string, number>();\n\n  for (const idx of indices) {\n    const file = idx.file;\n    let count = 0;\n    for (const intent of idx.intent) {\n      count++;\n      let files = commitToFiles.get(intent.hash);\n      if (!files) {\n        files = new Set();\n        commitToFiles.set(intent.hash, files);\n      }\n      files.add(file);\n    }\n    if (count > 0) {\n      fileCommitCounts.set(file, count);\n    }\n  }\n\n  // Step 2: Count shared commits per file pair\n  const pairCounts = new Map<string, number>();\n  for (const files of commitToFiles.values()) {\n    if (files.size < 2) continue;\n    const sorted = [...files].sort();\n    for (let i = 0; i < sorted.length; i++) {\n      for (let j = i + 1; j < sorted.length; j++) {\n        const key = `${sorted[i]}|${sorted[j]}`;\n        pairCounts.set(key, (pairCounts.get(key) ?? 0) + 1);\n      }\n    }\n  }\n\n  // Step 3: Calculate frequency and filter\n  const entries: CoChangeEntry[] = [];\n  for (const [key, sharedCommits] of pairCounts) {\n    if (sharedCommits < MIN_SHARED_COMMITS) continue;\n\n    const [file1, file2] = key.split('|') as [string, string];\n    const count1 = fileCommitCounts.get(file1) ?? 0;\n    const count2 = fileCommitCounts.get(file2) ?? 0;\n    const minCount = Math.min(count1, count2);\n    if (minCount === 0) continue;\n\n    const frequency = Math.round((sharedCommits / minCount) * 1000) / 1000;\n    if (frequency < MIN_FREQUENCY) continue;\n\n    entries.push({ file1, file2, sharedCommits, frequency });\n  }\n\n  entries.sort((a, b) => b.frequency - a.frequency || b.sharedCommits - a.sharedCommits);\n\n  return {\n    version: 1,\n    timestamp: Math.floor(Date.now() / 1000),\n    entries,\n  };\n}\n\nexport function loadCoChangeMap(matrix: CoChangeMatrix): Map<string, CoChangeEntry[]> {\n  const map = new Map<string, CoChangeEntry[]>();\n  for (const entry of matrix.entries) {\n    let list1 = map.get(entry.file1);\n    if (!list1) { list1 = []; map.set(entry.file1, list1); }\n    list1.push(entry);\n\n    let list2 = map.get(entry.file2);\n    if (!list2) { list2 = []; map.set(entry.file2, list2); }\n    list2.push(entry);\n  }\n  return 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package/dist/cli-router-Z5CSD6QN.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/adapters/language/tree-sitter-adapter.ts","../src/adapters/language/go-adapter.ts","../src/adapters/language/csharp-adapter.ts","../src/cli/index-command.ts","../src/core/staleness/content-hasher.ts","../src/adapters/language/ts-morph-adapter.ts","../src/adapters/language/language-adapter-registry.ts","../src/adapters/storage/json-index-writer.ts","../src/adapters/storage/schema-manager.ts","../src/cli/sync-command.ts","../src/cli/status-command.ts","../src/cli/verify-command.ts","../src/cli/init-command.ts","../src/cli/watch-command.ts","../src/adapters/watcher/chokidar-watcher-adapter.ts","../src/cli/cli-router.ts"],"sourcesContent":["import Parser from 'tree-sitter';\nimport type { Tree, SyntaxNode } from 'tree-sitter';\ntype Language = Parameters<InstanceType<typeof Parser>['setLanguage']>[0];\nimport { extname } from 'node:path';\nimport type { SymbolNode, GraphEdge, ComplexityMetrics, SymbolKind } from '../../core/types.js';\nimport type { ILanguageAdapter } from '../../ports/i-language-adapter.js';\n\nexport abstract class TreeSitterAdapter implements ILanguageAdapter {\n  abstract readonly extensions: readonly string[];\n  readonly tier = 'syntax' as const;\n\n  protected parser: Parser;\n  protected symbolRegistry = new Map<string, SymbolKind>();\n\n  constructor(language: Language) {\n    this.parser = new Parser();\n    this.parser.setLanguage(language);\n  }\n\n  isSupported(filePath: string): boolean {\n    const ext = extname(filePath).toLowerCase();\n    return (this.extensions as readonly string[]).includes(ext);\n  }\n\n  setSymbolRegistry(registry: Map<string, SymbolKind>): void {\n    this.symbolRegistry = registry;\n  }\n\n  protected parse(source: string): Tree {\n    return this.parser.parse(source);\n  }\n\n  protected buildSymbolId(filePath: string, name: string, kind: SymbolKind): string {\n    return `${filePath}::${name}::${kind}`;\n  }\n\n  protected nodeToLineRange(node: SyntaxNode): {\n    startLine: number;\n    endLine: number;\n    startOffset: number;\n    endOffset: number;\n  } {\n    return {\n      startLine: node.startPosition.row,\n      endLine: node.endPosition.row,\n      startOffset: node.startIndex,\n      endOffset: node.endIndex,\n    };\n  }\n\n  protected countCyclomaticComplexity(node: SyntaxNode, branchTypes: string[]): number {\n    let complexity = 1;\n    const visit = (n: SyntaxNode) => {\n      if (branchTypes.includes(n.type)) {\n        complexity++;\n      }\n      for (let i = 0; i < n.childCount; i++) {\n        visit(n.child(i)!);\n      }\n    };\n    visit(node);\n    return complexity;\n  }\n\n  abstract extractSymbols(filePath: string, source: string): SymbolNode[];\n  abstract extractEdges(filePath: string, source: string): GraphEdge[];\n  abstract extractComplexity(filePath: string, source: string): ComplexityMetrics[];\n}\n","import GoLanguage from 'tree-sitter-go';\nimport type { SyntaxNode } from 'tree-sitter';\nimport { TreeSitterAdapter } from './tree-sitter-adapter.js';\nimport type { SymbolNode, GraphEdge, ComplexityMetrics } from '../../core/types.js';\n\nconst GO_BRANCH_TYPES = [\n  'if_statement', 'for_statement',\n  'expression_switch_statement', 'type_switch_statement',\n  'expression_case', 'type_case',\n  'select_statement', 'communication_case',\n];\n\nexport class GoAdapter extends TreeSitterAdapter {\n  readonly extensions = ['.go'] as const;\n\n  constructor() {\n    super(GoLanguage);\n  }\n\n  extractSymbols(filePath: string, source: string): SymbolNode[] {\n    try {\n      const tree = this.parse(source);\n      const symbols: SymbolNode[] = [];\n\n      for (let i = 0; i < tree.rootNode.childCount; i++) {\n        const node = tree.rootNode.child(i)!;\n\n        if (node.type === 'function_declaration') {\n          const name = node.childForFieldName('name')?.text;\n          if (!name || !this.isExported(name)) continue;\n          const range = this.nodeToLineRange(node);\n          symbols.push({\n            symbolId: this.buildSymbolId(filePath, name, 'function'),\n            name,\n            kind: 'function',\n            ...range,\n          });\n        }\n\n        if (node.type === 'method_declaration') {\n          const methodName = node.childForFieldName('name')?.text;\n          if (!methodName || !this.isExported(methodName)) continue;\n          const receiverType = this.extractReceiverType(node);\n          const qualifiedName = receiverType ? `${receiverType}.${methodName}` : methodName;\n          const range = this.nodeToLineRange(node);\n          symbols.push({\n            symbolId: this.buildSymbolId(filePath, qualifiedName, 'method'),\n            name: qualifiedName,\n            kind: 'method',\n            ...range,\n          });\n        }\n\n        if (node.type === 'type_declaration') {\n          this.extractTypeSymbols(node, filePath, symbols);\n        }\n      }\n\n      return symbols;\n    } catch (err) {\n      console.error(`[ctxo:go] Symbol extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  extractEdges(filePath: string, source: string): GraphEdge[] {\n    try {\n      const tree = this.parse(source);\n      const edges: GraphEdge[] = [];\n      const firstExportedSymbol = this.findFirstExportedSymbolId(tree.rootNode, filePath);\n      if (!firstExportedSymbol) return edges;\n\n      for (let i = 0; i < tree.rootNode.childCount; i++) {\n        const node = tree.rootNode.child(i)!;\n\n        if (node.type === 'import_declaration') {\n          this.extractImportEdges(node, filePath, firstExportedSymbol, edges);\n        }\n      }\n\n      return edges;\n    } catch (err) {\n      console.error(`[ctxo:go] Edge extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  extractComplexity(filePath: string, source: string): ComplexityMetrics[] {\n    try {\n      const tree = this.parse(source);\n      const metrics: ComplexityMetrics[] = [];\n\n      for (let i = 0; i < tree.rootNode.childCount; i++) {\n        const node = tree.rootNode.child(i)!;\n\n        if (node.type === 'function_declaration') {\n          const name = node.childForFieldName('name')?.text;\n          if (!name || !this.isExported(name)) continue;\n          metrics.push({\n            symbolId: this.buildSymbolId(filePath, name, 'function'),\n            cyclomatic: this.countCyclomaticComplexity(node, GO_BRANCH_TYPES),\n          });\n        }\n\n        if (node.type === 'method_declaration') {\n          const methodName = node.childForFieldName('name')?.text;\n          if (!methodName || !this.isExported(methodName)) continue;\n          const receiverType = this.extractReceiverType(node);\n          const qualifiedName = receiverType ? `${receiverType}.${methodName}` : methodName;\n          metrics.push({\n            symbolId: this.buildSymbolId(filePath, qualifiedName, 'method'),\n            cyclomatic: this.countCyclomaticComplexity(node, GO_BRANCH_TYPES),\n          });\n        }\n      }\n\n      return metrics;\n    } catch (err) {\n      console.error(`[ctxo:go] Complexity extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  // ── Private helpers ─────────────────────────────────────────\n\n  private isExported(name: string): boolean {\n    return name.length > 0 && name[0]! === name[0]!.toUpperCase() && name[0]! !== name[0]!.toLowerCase();\n  }\n\n  private extractReceiverType(methodNode: SyntaxNode): string | undefined {\n    // method_declaration has parameter_list as first child (receiver)\n    const params = methodNode.child(1);\n    if (params?.type !== 'parameter_list') return undefined;\n\n    for (let i = 0; i < params.childCount; i++) {\n      const param = params.child(i)!;\n      if (param.type === 'parameter_declaration') {\n        // Find type identifier — may be pointer (*Type) or plain (Type)\n        const typeNode = param.childForFieldName('type');\n        if (typeNode) {\n          const text = typeNode.text;\n          return text.replace(/^\\*/, '');\n        }\n      }\n    }\n    return undefined;\n  }\n\n  private extractTypeSymbols(typeDecl: SyntaxNode, filePath: string, symbols: SymbolNode[]): void {\n    for (let i = 0; i < typeDecl.childCount; i++) {\n      const spec = typeDecl.child(i)!;\n      if (spec.type !== 'type_spec') continue;\n\n      const name = spec.childForFieldName('name')?.text;\n      if (!name || !this.isExported(name)) continue;\n\n      // Determine kind from the type body\n      const typeBody = spec.childForFieldName('type');\n      let kind: 'class' | 'interface' | 'type' = 'type';\n      if (typeBody?.type === 'struct_type') kind = 'class';\n      else if (typeBody?.type === 'interface_type') kind = 'interface';\n\n      const range = this.nodeToLineRange(spec);\n      symbols.push({\n        symbolId: this.buildSymbolId(filePath, name, kind),\n        name,\n        kind,\n        ...range,\n      });\n    }\n  }\n\n  private extractImportEdges(\n    importDecl: SyntaxNode,\n    _filePath: string,\n    fromSymbol: string,\n    edges: GraphEdge[],\n  ): void {\n    const visit = (node: SyntaxNode) => {\n      if (node.type === 'import_spec') {\n        const pathNode = node.childForFieldName('path') ?? node.child(0);\n        if (pathNode) {\n          const importPath = pathNode.text.replace(/\"/g, '');\n          edges.push({\n            from: fromSymbol,\n            to: `${importPath}::${importPath.split('/').pop()}::variable`,\n            kind: 'imports',\n          });\n        }\n      }\n      for (let i = 0; i < node.childCount; i++) {\n        visit(node.child(i)!);\n      }\n    };\n    visit(importDecl);\n  }\n\n  private findFirstExportedSymbolId(rootNode: SyntaxNode, filePath: string): string | undefined {\n    for (let i = 0; i < rootNode.childCount; i++) {\n      const node = rootNode.child(i)!;\n\n      if (node.type === 'function_declaration') {\n        const name = node.childForFieldName('name')?.text;\n        if (name && this.isExported(name)) return this.buildSymbolId(filePath, name, 'function');\n      }\n      if (node.type === 'type_declaration') {\n        for (let j = 0; j < node.childCount; j++) {\n          const spec = node.child(j)!;\n          if (spec.type === 'type_spec') {\n            const name = spec.childForFieldName('name')?.text;\n            if (name && this.isExported(name)) {\n              const typeBody = spec.childForFieldName('type');\n              const kind = typeBody?.type === 'struct_type' ? 'class' : typeBody?.type === 'interface_type' ? 'interface' : 'type';\n              return this.buildSymbolId(filePath, name, kind);\n            }\n          }\n        }\n      }\n    }\n    return undefined;\n  }\n}\n","import CSharpLanguage from 'tree-sitter-c-sharp';\nimport type { SyntaxNode } from 'tree-sitter';\nimport { TreeSitterAdapter } from './tree-sitter-adapter.js';\nimport type { SymbolNode, GraphEdge, ComplexityMetrics, SymbolKind } from '../../core/types.js';\n\nconst CSHARP_BRANCH_TYPES = [\n  'if_statement', 'for_statement', 'foreach_statement',\n  'while_statement', 'do_statement', 'switch_section',\n  'catch_clause', 'conditional_expression',\n];\n\nexport class CSharpAdapter extends TreeSitterAdapter {\n  readonly extensions = ['.cs'] as const;\n\n  constructor() {\n    super(CSharpLanguage);\n  }\n\n  extractSymbols(filePath: string, source: string): SymbolNode[] {\n    try {\n      const tree = this.parse(source);\n      const symbols: SymbolNode[] = [];\n      this.visitSymbols(tree.rootNode, filePath, '', symbols);\n      return symbols;\n    } catch (err) {\n      console.error(`[ctxo:csharp] Symbol extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  extractEdges(filePath: string, source: string): GraphEdge[] {\n    try {\n      const tree = this.parse(source);\n      const edges: GraphEdge[] = [];\n      const symbols = this.extractSymbols(filePath, source);\n      const firstSymbol = symbols.length > 0 ? symbols[0]!.symbolId : undefined;\n      if (!firstSymbol) return edges;\n\n      this.visitEdges(tree.rootNode, filePath, firstSymbol, '', edges);\n      return edges;\n    } catch (err) {\n      console.error(`[ctxo:csharp] Edge extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  extractComplexity(filePath: string, source: string): ComplexityMetrics[] {\n    try {\n      const tree = this.parse(source);\n      const metrics: ComplexityMetrics[] = [];\n      this.visitComplexity(tree.rootNode, filePath, '', metrics);\n      return metrics;\n    } catch (err) {\n      console.error(`[ctxo:csharp] Complexity extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  // ── Symbol visitor ──────────────────────────────────────────\n\n  private visitSymbols(\n    node: SyntaxNode,\n    filePath: string,\n    namespace: string,\n    symbols: SymbolNode[],\n  ): void {\n    if (node.type === 'namespace_declaration') {\n      const name = node.childForFieldName('name')?.text ?? '';\n      const ns = namespace ? `${namespace}.${name}` : name;\n      for (let i = 0; i < node.childCount; i++) {\n        this.visitSymbols(node.child(i)!, filePath, ns, symbols);\n      }\n      return;\n    }\n\n    if (node.type === 'declaration_list') {\n      for (let i = 0; i < node.childCount; i++) {\n        this.visitSymbols(node.child(i)!, filePath, namespace, symbols);\n      }\n      return;\n    }\n\n    const typeMapping: Record<string, SymbolKind> = {\n      class_declaration: 'class',\n      struct_declaration: 'class',\n      record_declaration: 'class',\n      interface_declaration: 'interface',\n      enum_declaration: 'type',\n    };\n\n    const kind = typeMapping[node.type];\n    if (kind) {\n      if (!this.isPublic(node)) return;\n      const name = node.childForFieldName('name')?.text;\n      if (!name) return;\n\n      const qualifiedName = namespace ? `${namespace}.${name}` : name;\n      const range = this.nodeToLineRange(node);\n      symbols.push({\n        symbolId: this.buildSymbolId(filePath, qualifiedName, kind),\n        name: qualifiedName,\n        kind,\n        ...range,\n      });\n\n      // Extract methods inside the class/struct/record\n      if (kind === 'class') {\n        this.extractMethodSymbols(node, filePath, qualifiedName, symbols);\n      }\n      return;\n    }\n\n    // Recurse into compilation_unit and other containers\n    for (let i = 0; i < node.childCount; i++) {\n      this.visitSymbols(node.child(i)!, filePath, namespace, symbols);\n    }\n  }\n\n  private extractMethodSymbols(\n    classNode: SyntaxNode,\n    filePath: string,\n    className: string,\n    symbols: SymbolNode[],\n  ): void {\n    const declList = classNode.children.find(c => c.type === 'declaration_list');\n    if (!declList) return;\n\n    for (let i = 0; i < declList.childCount; i++) {\n      const child = declList.child(i)!;\n      if (child.type !== 'method_declaration' && child.type !== 'constructor_declaration') continue;\n      if (!this.isPublic(child)) continue;\n\n      const name = child.childForFieldName('name')?.text;\n      if (!name) continue;\n\n      const paramCount = this.countParameters(child);\n      const qualifiedName = `${className}.${name}(${paramCount})`;\n      const range = this.nodeToLineRange(child);\n      symbols.push({\n        symbolId: this.buildSymbolId(filePath, qualifiedName, 'method'),\n        name: qualifiedName,\n        kind: 'method',\n        ...range,\n      });\n    }\n  }\n\n  // ── Edge visitor ────────────────────────────────────────────\n\n  private visitEdges(\n    node: SyntaxNode,\n    filePath: string,\n    fromSymbol: string,\n    namespace: string,\n    edges: GraphEdge[],\n  ): void {\n    if (node.type === 'using_directive') {\n      const nameNode = node.children.find(c => c.type === 'identifier' || c.type === 'qualified_name');\n      if (nameNode) {\n        edges.push({\n          from: fromSymbol,\n          to: `${nameNode.text}::${nameNode.text.split('.').pop()}::variable`,\n          kind: 'imports',\n        });\n      }\n      return;\n    }\n\n    if (node.type === 'namespace_declaration') {\n      const name = node.childForFieldName('name')?.text ?? '';\n      const ns = namespace ? `${namespace}.${name}` : name;\n      for (let i = 0; i < node.childCount; i++) {\n        this.visitEdges(node.child(i)!, filePath, fromSymbol, ns, edges);\n      }\n      return;\n    }\n\n    if (node.type === 'class_declaration' || node.type === 'struct_declaration') {\n      if (!this.isPublic(node)) return;\n      const name = node.childForFieldName('name')?.text;\n      if (!name) return;\n\n      const qualifiedName = namespace ? `${namespace}.${name}` : name;\n      const classSymbolId = this.buildSymbolId(filePath, qualifiedName, 'class');\n\n      // Check base_list for extends/implements\n      const baseList = node.children.find(c => c.type === 'base_list');\n      if (baseList) {\n        for (let i = 0; i < baseList.childCount; i++) {\n          const child = baseList.child(i)!;\n          if (child.type === 'identifier' || child.type === 'qualified_name') {\n            const baseName = child.text;\n            // Heuristic: I-prefix = interface → implements, otherwise extends\n            const edgeKind = baseName.match(/^I[A-Z]/) ? 'implements' : 'extends';\n            const targetKind = edgeKind === 'implements' ? 'interface' : 'class';\n            edges.push({\n              from: classSymbolId,\n              to: this.resolveBaseType(baseName, namespace, targetKind),\n              kind: edgeKind,\n            });\n          }\n        }\n      }\n    }\n\n    for (let i = 0; i < node.childCount; i++) {\n      this.visitEdges(node.child(i)!, filePath, fromSymbol, namespace, edges);\n    }\n  }\n\n  // ── Complexity visitor ──────────────────────────────────────\n\n  private visitComplexity(\n    node: SyntaxNode,\n    filePath: string,\n    namespace: string,\n    metrics: ComplexityMetrics[],\n  ): void {\n    if (node.type === 'namespace_declaration') {\n      const name = node.childForFieldName('name')?.text ?? '';\n      const ns = namespace ? `${namespace}.${name}` : name;\n      for (let i = 0; i < node.childCount; i++) {\n        this.visitComplexity(node.child(i)!, filePath, ns, metrics);\n      }\n      return;\n    }\n\n    const typeMapping: Record<string, true> = {\n      class_declaration: true,\n      struct_declaration: true,\n      record_declaration: true,\n    };\n\n    if (typeMapping[node.type]) {\n      if (!this.isPublic(node)) return;\n      const className = node.childForFieldName('name')?.text;\n      if (!className) return;\n\n      const qualifiedClass = namespace ? `${namespace}.${className}` : className;\n      const declList = node.children.find(c => c.type === 'declaration_list');\n      if (!declList) return;\n\n      for (let i = 0; i < declList.childCount; i++) {\n        const child = declList.child(i)!;\n        if (child.type !== 'method_declaration') continue;\n        if (!this.isPublic(child)) continue;\n\n        const methodName = child.childForFieldName('name')?.text;\n        if (!methodName) continue;\n\n        const paramCount = this.countParameters(child);\n        metrics.push({\n          symbolId: this.buildSymbolId(filePath, `${qualifiedClass}.${methodName}(${paramCount})`, 'method'),\n          cyclomatic: this.countCyclomaticComplexity(child, CSHARP_BRANCH_TYPES),\n        });\n      }\n      return;\n    }\n\n    for (let i = 0; i < node.childCount; i++) {\n      this.visitComplexity(node.child(i)!, filePath, namespace, metrics);\n    }\n  }\n\n  // ── Helpers ─────────────────────────────────────────────────\n\n  private countParameters(methodNode: SyntaxNode): number {\n    const paramList = methodNode.childForFieldName('parameters');\n    if (!paramList) return 0;\n    let count = 0;\n    for (let i = 0; i < paramList.childCount; i++) {\n      if (paramList.child(i)!.type === 'parameter') count++;\n    }\n    return count;\n  }\n\n  private isPublic(node: SyntaxNode): boolean {\n    for (let i = 0; i < node.childCount; i++) {\n      const child = node.child(i)!;\n      if (child.type === 'modifier' && child.text === 'public') return true;\n    }\n    return false;\n  }\n\n  private resolveBaseType(baseName: string, namespace: string, defaultKind: SymbolKind): string {\n    // Check symbol registry first\n    const prefix = namespace ? `${namespace}.${baseName}` : baseName;\n    for (const [id] of this.symbolRegistry) {\n      if (id.includes(`::${prefix}::`)) return id;\n      if (id.includes(`::${baseName}::`)) return id;\n    }\n    // Fallback: assume same namespace\n    const qualifiedName = namespace ? `${namespace}.${baseName}` : baseName;\n    return `${qualifiedName}::${baseName}::${defaultKind}`;\n  }\n}\n","import { execFileSync } from 'node:child_process';\nimport { readFileSync, writeFileSync, existsSync, statSync, readdirSync } from 'node:fs';\nimport { join, relative, extname } from 'node:path';\nimport { ContentHasher } from '../core/staleness/content-hasher.js';\nimport { TsMorphAdapter } from '../adapters/language/ts-morph-adapter.js';\nimport { LanguageAdapterRegistry } from '../adapters/language/language-adapter-registry.js';\nimport { JsonIndexWriter } from '../adapters/storage/json-index-writer.js';\nimport { SqliteStorageAdapter } from '../adapters/storage/sqlite-storage-adapter.js';\nimport { SchemaManager } from '../adapters/storage/schema-manager.js';\nimport { SimpleGitAdapter } from '../adapters/git/simple-git-adapter.js';\nimport { RevertDetector } from '../core/why-context/revert-detector.js';\nimport { aggregateCoChanges } from '../core/co-change/co-change-analyzer.js';\nimport type { FileIndex, SymbolKind } from '../core/types.js';\n\nexport class IndexCommand {\n  private readonly projectRoot: string;\n  ctxoRoot: string;\n  private supportedExtensions: Set<string>;\n\n  constructor(projectRoot: string, ctxoRoot?: string) {\n    this.projectRoot = projectRoot;\n    this.ctxoRoot = ctxoRoot ?? join(projectRoot, '.ctxo');\n    this.supportedExtensions = new Set(['.ts', '.tsx', '.js', '.jsx', '.go', '.cs']);\n  }\n\n  async run(options: { file?: string; check?: boolean; skipSideEffects?: boolean; skipHistory?: boolean; maxHistory?: number } = {}): Promise<void> {\n    if (options.check) {\n      // Delegate to verify logic: hash-based freshness check\n      return this.runCheck();\n    }\n\n    // Set up adapters\n    const registry = new LanguageAdapterRegistry();\n    const tsMorphAdapter = new TsMorphAdapter();\n    registry.register(tsMorphAdapter);\n    this.registerTreeSitterAdapters(registry);\n    this.supportedExtensions = registry.getSupportedExtensions();\n\n    const writer = new JsonIndexWriter(this.ctxoRoot);\n    const schemaManager = new SchemaManager(this.ctxoRoot);\n    const hasher = new ContentHasher();\n    const gitAdapter = new SimpleGitAdapter(this.projectRoot);\n    const revertDetector = new RevertDetector();\n\n    // Discover files (single file, monorepo workspaces, or full project)\n    let files: string[];\n    if (options.file) {\n      const fullPath = join(this.projectRoot, options.file);\n      files = [fullPath];\n      console.error(`[ctxo] Incremental re-index: ${options.file}`);\n    } else {\n      // Check for monorepo workspaces — discover files across all roots\n      const workspaces = this.discoverWorkspaces();\n      files = [];\n      for (const ws of workspaces) {\n        const wsFiles = this.discoverFilesIn(ws);\n        files.push(...wsFiles);\n      }\n      console.error(`[ctxo] Building codebase index... Found ${files.length} source files`);\n    }\n\n    // Phase 1a: Extract symbols (CPU-bound, builds symbol registry for edge resolution)\n    const symbolRegistry = new Map<string, SymbolKind>();\n    const pendingIndices: Array<{\n      relativePath: string;\n      source: string;\n      fileIndex: FileIndex;\n    }> = [];\n    let processed = 0;\n\n    for (const filePath of files) {\n      const adapter = registry.getAdapter(filePath);\n      if (!adapter) continue;\n\n      const relativePath = relative(this.projectRoot, filePath).replace(/\\\\/g, '/');\n\n      try {\n        const source = readFileSync(filePath, 'utf-8');\n        const lastModified = Math.floor(Date.now() / 1000);\n\n        const symbols = adapter.extractSymbols(relativePath, source);\n        const complexity = adapter.extractComplexity(relativePath, source);\n\n        // Build symbol registry for accurate edge resolution\n        for (const sym of symbols) {\n          symbolRegistry.set(sym.symbolId, sym.kind);\n        }\n\n        pendingIndices.push({\n          relativePath,\n          source,\n          fileIndex: {\n            file: relativePath,\n            lastModified,\n            contentHash: hasher.hash(source),\n            symbols,\n            edges: [],\n            complexity,\n            intent: [],\n            antiPatterns: [],\n          },\n        });\n\n        processed++;\n        if (processed % 50 === 0) {\n          console.error(`[ctxo] Processed ${processed}/${files.length} files (symbols)`);\n        }\n      } catch (err) {\n        console.error(`[ctxo] Skipped ${relativePath}: ${(err as Error).message}`);\n      }\n    }\n\n    // Pre-load all sources into ts-morph for cross-file resolution\n    const allSources = new Map<string, string>();\n    for (const entry of pendingIndices) {\n      allSources.set(entry.relativePath, entry.source);\n    }\n    tsMorphAdapter.loadProjectSources(allSources);\n\n    // Phase 1b: Extract edges (uses symbol registry for correct kind resolution)\n    for (const entry of pendingIndices) {\n      const adapter = registry.getAdapter(entry.relativePath);\n      if (!adapter) continue;\n\n      try {\n        adapter.setSymbolRegistry?.(symbolRegistry);\n        entry.fileIndex.edges = adapter.extractEdges(entry.relativePath, entry.source);\n      } catch (err) {\n        console.error(`[ctxo] Edge extraction failed for ${entry.relativePath}: ${(err as Error).message}`);\n      }\n    }\n\n    // Clean up pre-loaded sources\n    tsMorphAdapter.clearProjectSources();\n\n    // Phase 2: Batch git history (single git call for all files)\n    if (!options.skipHistory && pendingIndices.length > 0) {\n      const maxHistory = options.maxHistory ?? 20;\n      const batchHistory = await gitAdapter.getBatchHistory?.(maxHistory) ?? new Map<string, import('../core/types.js').CommitRecord[]>();\n\n      for (const { relativePath, fileIndex } of pendingIndices) {\n        const commits = batchHistory.get(relativePath) ?? [];\n        fileIndex.intent = commits.map((c) => ({\n          hash: c.hash,\n          message: c.message,\n          date: c.date,\n          kind: 'commit' as const,\n        }));\n        fileIndex.antiPatterns = revertDetector.detect(commits);\n      }\n    }\n\n    // Phase 2b: Aggregate co-change data from git history\n    if (!options.skipHistory && pendingIndices.length > 0) {\n      const fileIndices = pendingIndices.map(e => e.fileIndex);\n      const coChangeMatrix = aggregateCoChanges(fileIndices);\n      writer.writeCoChanges(coChangeMatrix);\n      console.error(`[ctxo] Co-change analysis: ${coChangeMatrix.entries.length} file pairs detected`);\n    }\n\n    // Phase 3: Write all indices\n    const indices: FileIndex[] = [];\n    for (const { fileIndex } of pendingIndices) {\n      writer.write(fileIndex);\n      indices.push(fileIndex);\n    }\n\n    // Write schema version\n    schemaManager.writeVersion();\n\n    // Populate SQLite cache (skip rebuildFromJson since we just wrote the JSON)\n    const storage = new SqliteStorageAdapter(this.ctxoRoot);\n    try {\n      await storage.initEmpty();\n      storage.bulkWrite(indices);\n    } finally {\n      storage.close();\n    }\n\n    // Ensure .ctxo/.cache/ is in .gitignore (skip during verify runs)\n    if (!options.skipSideEffects) {\n      this.ensureGitignore();\n    }\n\n    console.error(`[ctxo] Index complete: ${processed} files indexed`);\n  }\n\n  private registerTreeSitterAdapters(registry: LanguageAdapterRegistry): void {\n    try {\n      // eslint-disable-next-line @typescript-eslint/no-require-imports\n      const { GoAdapter } = require('../adapters/language/go-adapter.js');\n      registry.register(new GoAdapter());\n    } catch {\n      console.error('[ctxo] Go adapter unavailable (tree-sitter-go not installed)');\n    }\n    try {\n      // eslint-disable-next-line @typescript-eslint/no-require-imports\n      const { CSharpAdapter } = require('../adapters/language/csharp-adapter.js');\n      registry.register(new CSharpAdapter());\n    } catch {\n      console.error('[ctxo] C# adapter unavailable (tree-sitter-c-sharp not installed)');\n    }\n  }\n\n  private discoverFilesIn(root: string): string[] {\n    try {\n      const output = execFileSync('git', ['ls-files', '--cached', '--others', '--exclude-standard'], {\n        cwd: root,\n        encoding: 'utf-8',\n        maxBuffer: 10 * 1024 * 1024,\n      });\n\n      return output\n        .split('\\n')\n        .map((line) => line.trim())\n        .filter((line) => line.length > 0)\n        .filter((line) => this.isSupportedExtension(line))\n        .map((line) => join(root, line));\n    } catch {\n      console.error(`[ctxo] git ls-files failed for ${root}`);\n      return [];\n    }\n  }\n\n  private discoverWorkspaces(): string[] {\n    const pkgPath = join(this.projectRoot, 'package.json');\n    if (!existsSync(pkgPath)) return [this.projectRoot];\n\n    try {\n      const pkg = JSON.parse(readFileSync(pkgPath, 'utf-8'));\n      const workspaces: string[] | undefined = Array.isArray(pkg.workspaces)\n        ? pkg.workspaces\n        : pkg.workspaces?.packages;\n\n      if (!workspaces || workspaces.length === 0) return [this.projectRoot];\n\n      // Resolve workspace patterns (supports simple globs like packages/*)\n      const resolved: string[] = [];\n      for (const ws of workspaces) {\n        if (ws.endsWith('/*') || ws.endsWith('\\\\*')) {\n          // Glob: packages/* → list subdirectories of packages/\n          const parentDir = join(this.projectRoot, ws.slice(0, -2));\n          if (existsSync(parentDir)) {\n            for (const entry of readdirSync(parentDir, { withFileTypes: true })) {\n              if (entry.isDirectory()) {\n                resolved.push(join(parentDir, entry.name));\n              }\n            }\n          }\n        } else {\n          // Literal path\n          const wsPath = join(this.projectRoot, ws);\n          if (existsSync(wsPath)) {\n            resolved.push(wsPath);\n          }\n        }\n      }\n\n      if (resolved.length === 0) return [this.projectRoot];\n\n      console.error(`[ctxo] Monorepo detected: ${resolved.length} workspace(s)`);\n      return resolved;\n    } catch {\n      return [this.projectRoot];\n    }\n  }\n\n  private isSupportedExtension(filePath: string): boolean {\n    const ext = extname(filePath).toLowerCase();\n    return this.supportedExtensions.has(ext);\n  }\n\n  private async runCheck(): Promise<void> {\n    console.error('[ctxo] Checking index freshness...');\n\n    // Register adapters so supportedExtensions includes .go/.cs\n    const registry = new LanguageAdapterRegistry();\n    registry.register(new TsMorphAdapter());\n    this.registerTreeSitterAdapters(registry);\n    this.supportedExtensions = registry.getSupportedExtensions();\n\n    const hasher = new ContentHasher();\n    const files = this.discoverFilesIn(this.projectRoot);\n    const reader = new (await import('../adapters/storage/json-index-reader.js')).JsonIndexReader(this.ctxoRoot);\n    const indices = reader.readAll();\n    const indexedMap = new Map(indices.map((i) => [i.file, i]));\n\n    let staleCount = 0;\n\n    for (const filePath of files) {\n      if (!this.isSupportedExtension(filePath)) continue;\n\n      const relativePath = relative(this.projectRoot, filePath).replace(/\\\\/g, '/');\n      const indexed = indexedMap.get(relativePath);\n\n      if (!indexed) {\n        console.error(`[ctxo] NOT INDEXED: ${relativePath}`);\n        staleCount++;\n        continue;\n      }\n\n      // Guard: file may be deleted from disk but still tracked by git\n      if (!existsSync(filePath)) {\n        console.error(`[ctxo] DELETED: ${relativePath}`);\n        staleCount++;\n        continue;\n      }\n\n      // Fast path: mtime check (skip hash if mtime hasn't changed)\n      const mtime = Math.floor(statSync(filePath).mtimeMs / 1000);\n      if (mtime <= indexed.lastModified) continue;\n\n      // Slow path: hash-based verification (handles git checkout, cp -p, CI)\n      if (indexed.contentHash) {\n        const source = readFileSync(filePath, 'utf-8');\n        const currentHash = hasher.hash(source);\n        if (currentHash === indexed.contentHash) continue;\n      }\n\n      console.error(`[ctxo] STALE: ${relativePath}`);\n      staleCount++;\n    }\n\n    if (staleCount > 0) {\n      console.error(`[ctxo] ${staleCount} file(s) need re-indexing. Run \"ctxo index\"`);\n      process.exit(1);\n    }\n\n    console.error('[ctxo] Index is up to date');\n  }\n\n  private ensureGitignore(): void {\n    const gitignorePath = join(this.projectRoot, '.gitignore');\n    const cachePattern = '.ctxo/.cache/';\n    const suffix = `\\n# Ctxo local cache (never committed)\\n${cachePattern}\\n`;\n\n    // Read-modify-write atomically to avoid TOCTOU race\n    const existing = existsSync(gitignorePath) ? readFileSync(gitignorePath, 'utf-8') : '';\n    if (existing.includes(cachePattern)) return;\n\n    writeFileSync(gitignorePath, existing + suffix, 'utf-8');\n    console.error('[ctxo] Added .ctxo/.cache/ to .gitignore');\n  }\n}\n","import { createHash } from 'node:crypto';\n\nexport class ContentHasher {\n  hash(content: string): string {\n    return createHash('sha256').update(content, 'utf-8').digest('hex');\n  }\n}\n","import {\n  Project,\n  SyntaxKind,\n  Node,\n  type SourceFile,\n  type FunctionDeclaration,\n  type MethodDeclaration,\n  ScriptTarget,\n} from 'ts-morph';\nimport { extname, dirname, join, normalize } from 'node:path';\nimport { type SymbolNode, type GraphEdge, type ComplexityMetrics, type SymbolKind, SYMBOL_KINDS } from '../../core/types.js';\nimport type { ILanguageAdapter } from '../../ports/i-language-adapter.js';\n\nconst SUPPORTED_EXTENSIONS = ['.ts', '.tsx', '.js', '.jsx'] as const;\n\nexport class TsMorphAdapter implements ILanguageAdapter {\n  readonly extensions = SUPPORTED_EXTENSIONS;\n  readonly tier = 'full' as const;\n\n  private readonly project: Project;\n  private symbolRegistry = new Map<string, SymbolKind>();\n  private projectPreloaded = false;\n\n  constructor() {\n    this.project = new Project({\n      compilerOptions: {\n        target: ScriptTarget.ES2022,\n        allowJs: true,\n        jsx: 2, // React\n        skipLibCheck: true,\n      },\n      useInMemoryFileSystem: true,\n    });\n  }\n\n  isSupported(filePath: string): boolean {\n    const ext = extname(filePath).toLowerCase();\n    return (SUPPORTED_EXTENSIONS as readonly string[]).includes(ext);\n  }\n\n  setSymbolRegistry(registry: Map<string, SymbolKind>): void {\n    this.symbolRegistry = registry;\n  }\n\n  loadProjectSources(files: Map<string, string>): void {\n    for (const [filePath, source] of files) {\n      try {\n        const existing = this.project.getSourceFile(filePath);\n        if (existing) this.project.removeSourceFile(existing);\n        this.project.createSourceFile(filePath, source, { overwrite: true });\n      } catch (err) {\n        console.error(`[ctxo:ts-morph] Failed to preload ${filePath}: ${(err as Error).message}`);\n      }\n    }\n    this.projectPreloaded = true;\n  }\n\n  clearProjectSources(): void {\n    for (const sf of this.project.getSourceFiles()) {\n      this.project.removeSourceFile(sf);\n    }\n    this.projectPreloaded = false;\n  }\n\n  extractSymbols(filePath: string, source: string): SymbolNode[] {\n    const sourceFile = this.parseSource(filePath, source);\n    if (!sourceFile) return [];\n\n    try {\n      const symbols: SymbolNode[] = [];\n\n      this.extractFunctions(sourceFile, filePath, symbols);\n      this.extractClasses(sourceFile, filePath, symbols);\n      this.extractInterfaces(sourceFile, filePath, symbols);\n      this.extractTypeAliases(sourceFile, filePath, symbols);\n      this.extractVariables(sourceFile, filePath, symbols);\n\n      return symbols;\n    } catch (err) {\n      console.error(`[ctxo:ts-morph] Symbol extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    } finally {\n      this.cleanupSourceFile(filePath);\n    }\n  }\n\n  extractEdges(filePath: string, source: string): GraphEdge[] {\n    const sourceFile = this.parseSource(filePath, source);\n    if (!sourceFile) return [];\n\n    try {\n      const edges: GraphEdge[] = [];\n\n      this.extractImportEdges(sourceFile, filePath, edges);\n      this.extractInheritanceEdges(sourceFile, filePath, edges);\n      this.extractCallEdges(sourceFile, filePath, edges);\n      this.extractReferenceEdges(sourceFile, filePath, edges);\n\n      return edges;\n    } catch (err) {\n      console.error(`[ctxo:ts-morph] Edge extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    } finally {\n      if (!this.projectPreloaded) {\n        this.cleanupSourceFile(filePath);\n      }\n    }\n  }\n\n  extractComplexity(filePath: string, source: string): ComplexityMetrics[] {\n    const sourceFile = this.parseSource(filePath, source);\n    if (!sourceFile) return [];\n\n    try {\n      const metrics: ComplexityMetrics[] = [];\n\n      for (const fn of sourceFile.getFunctions()) {\n        if (!this.isExported(fn)) continue;\n        const name = fn.getName();\n        if (!name) continue;\n        const symbolId = this.buildSymbolId(filePath, name, 'function');\n        metrics.push({ symbolId, cyclomatic: this.countCyclomaticComplexity(fn) });\n      }\n\n      for (const cls of sourceFile.getClasses()) {\n        const className = cls.getName();\n        if (!className || !this.isExported(cls)) continue;\n\n        for (const method of cls.getMethods()) {\n          const methodName = method.getName();\n          const symbolId = this.buildSymbolId(filePath, `${className}.${methodName}`, 'method');\n          metrics.push({ symbolId, cyclomatic: this.countCyclomaticComplexity(method) });\n        }\n      }\n\n      return metrics;\n    } catch (err) {\n      console.error(`[ctxo:ts-morph] Complexity extraction failed for ${filePath}: ${(err as Error).message}`);\n      return [];\n    } finally {\n      this.cleanupSourceFile(filePath);\n    }\n  }\n\n  // ── Symbol Extraction ───────────────────────────────────────\n\n  private extractFunctions(\n    sourceFile: SourceFile,\n    filePath: string,\n    symbols: SymbolNode[],\n  ): void {\n    for (const fn of sourceFile.getFunctions()) {\n      if (!this.isExported(fn)) continue;\n      const name = fn.getName();\n      if (!name) continue;\n\n      symbols.push({\n        symbolId: this.buildSymbolId(filePath, name, 'function'),\n        name,\n        kind: 'function',\n        startLine: fn.getStartLineNumber() - 1,\n        endLine: fn.getEndLineNumber() - 1,\n        startOffset: fn.getStart(),\n        endOffset: fn.getEnd(),\n      });\n    }\n  }\n\n  private extractClasses(\n    sourceFile: SourceFile,\n    filePath: string,\n    symbols: SymbolNode[],\n  ): void {\n    for (const cls of sourceFile.getClasses()) {\n      const name = cls.getName();\n      if (!name || !this.isExported(cls)) continue;\n\n      symbols.push({\n        symbolId: this.buildSymbolId(filePath, name, 'class'),\n        name,\n        kind: 'class',\n        startLine: cls.getStartLineNumber() - 1,\n        endLine: cls.getEndLineNumber() - 1,\n        startOffset: cls.getStart(),\n        endOffset: cls.getEnd(),\n      });\n\n      // Extract methods\n      for (const method of cls.getMethods()) {\n        const methodName = method.getName();\n        symbols.push({\n          symbolId: this.buildSymbolId(filePath, `${name}.${methodName}`, 'method'),\n          name: `${name}.${methodName}`,\n          kind: 'method',\n          startLine: method.getStartLineNumber() - 1,\n          endLine: method.getEndLineNumber() - 1,\n          startOffset: method.getStart(),\n          endOffset: method.getEnd(),\n        });\n      }\n    }\n  }\n\n  private extractInterfaces(\n    sourceFile: SourceFile,\n    filePath: string,\n    symbols: SymbolNode[],\n  ): void {\n    for (const iface of sourceFile.getInterfaces()) {\n      if (!this.isExported(iface)) continue;\n      const name = iface.getName();\n\n      symbols.push({\n        symbolId: this.buildSymbolId(filePath, name, 'interface'),\n        name,\n        kind: 'interface',\n        startLine: iface.getStartLineNumber() - 1,\n        endLine: iface.getEndLineNumber() - 1,\n        startOffset: iface.getStart(),\n        endOffset: iface.getEnd(),\n      });\n    }\n  }\n\n  private extractTypeAliases(\n    sourceFile: SourceFile,\n    filePath: string,\n    symbols: SymbolNode[],\n  ): void {\n    for (const typeAlias of sourceFile.getTypeAliases()) {\n      if (!this.isExported(typeAlias)) continue;\n      const name = typeAlias.getName();\n\n      symbols.push({\n        symbolId: this.buildSymbolId(filePath, name, 'type'),\n        name,\n        kind: 'type',\n        startLine: typeAlias.getStartLineNumber() - 1,\n        endLine: typeAlias.getEndLineNumber() - 1,\n        startOffset: typeAlias.getStart(),\n        endOffset: typeAlias.getEnd(),\n      });\n    }\n  }\n\n  private extractVariables(\n    sourceFile: SourceFile,\n    filePath: string,\n    symbols: SymbolNode[],\n  ): void {\n    for (const stmt of sourceFile.getVariableStatements()) {\n      if (!this.isExported(stmt)) continue;\n\n      for (const decl of stmt.getDeclarations()) {\n        const name = decl.getName();\n\n        symbols.push({\n          symbolId: this.buildSymbolId(filePath, name, 'variable'),\n          name,\n          kind: 'variable',\n          startLine: stmt.getStartLineNumber() - 1,\n          endLine: stmt.getEndLineNumber() - 1,\n          startOffset: decl.getStart(),\n          endOffset: decl.getEnd(),\n        });\n      }\n    }\n  }\n\n  // ── Edge Extraction ─────────────────────────────────────────\n\n  private extractImportEdges(\n    sourceFile: SourceFile,\n    filePath: string,\n    edges: GraphEdge[],\n  ): void {\n    // BUG-1 FIX: use sourceFile directly instead of project lookup (file may be cleaned up)\n    const fileSymbolId = this.buildSymbolId(filePath, sourceFile.getBaseName().replace(/\\.[^.]+$/, ''), 'variable');\n    const fromSymbols = this.getExportedSymbolIds(sourceFile, filePath);\n    const fromSymbol = fromSymbols.length > 0 ? fromSymbols[0]! : fileSymbolId;\n\n    for (const imp of sourceFile.getImportDeclarations()) {\n      const moduleSpecifier = imp.getModuleSpecifierValue();\n\n      // Only track local imports (relative paths)\n      if (!moduleSpecifier.startsWith('.') && !moduleSpecifier.startsWith('/')) {\n        continue;\n      }\n\n      // Resolve relative import to project-relative path\n      const normalizedTarget = this.resolveRelativeImport(filePath, moduleSpecifier);\n\n      // SCHEMA-40 FIX: detect type-only imports\n      const isTypeOnly = imp.isTypeOnly();\n\n      for (const named of imp.getNamedImports()) {\n        const importedName = named.getName();\n        const edge: GraphEdge = {\n          from: fromSymbol,\n          to: this.resolveImportTarget(normalizedTarget, importedName),\n          kind: 'imports',\n        };\n        if (isTypeOnly || named.isTypeOnly()) edge.typeOnly = true;\n        edges.push(edge);\n      }\n\n      const defaultImport = imp.getDefaultImport();\n      if (defaultImport) {\n        const edge: GraphEdge = {\n          from: fromSymbol,\n          to: this.resolveImportTarget(normalizedTarget, defaultImport.getText()),\n          kind: 'imports',\n        };\n        if (isTypeOnly) edge.typeOnly = true;\n        edges.push(edge);\n      }\n\n      // GAP-3 FIX: namespace imports (import * as X from './mod')\n      const nsImport = imp.getNamespaceImport();\n      if (nsImport) {\n        const edge: GraphEdge = {\n          from: fromSymbol,\n          to: this.buildSymbolId(normalizedTarget, nsImport.getText(), 'variable'),\n          kind: 'imports',\n        };\n        if (isTypeOnly) edge.typeOnly = true;\n        edges.push(edge);\n      }\n    }\n  }\n\n  private extractInheritanceEdges(\n    sourceFile: SourceFile,\n    filePath: string,\n    edges: GraphEdge[],\n  ): void {\n    for (const cls of sourceFile.getClasses()) {\n      const className = cls.getName();\n      if (!className || !this.isExported(cls)) continue;\n\n      const classSymbolId = this.buildSymbolId(filePath, className, 'class');\n\n      // extends\n      const baseClass = cls.getExtends();\n      if (baseClass) {\n        // BUG-17 FIX: strip generic type arguments (Base<string> → Base)\n        const baseName = baseClass.getExpression().getText().replace(/<.*>$/, '');\n        edges.push({\n          from: classSymbolId,\n          to: this.resolveSymbolReference(sourceFile, baseName, 'class'),\n          kind: 'extends',\n        });\n      }\n\n      // implements\n      for (const impl of cls.getImplements()) {\n        // BUG-18 FIX: strip generic type arguments (IRepo<User> → IRepo)\n        const ifaceName = impl.getExpression().getText().replace(/<.*>$/, '');\n        edges.push({\n          from: classSymbolId,\n          to: this.resolveSymbolReference(sourceFile, ifaceName, 'interface'),\n          kind: 'implements',\n        });\n      }\n    }\n  }\n\n  private extractCallEdges(\n    sourceFile: SourceFile,\n    filePath: string,\n    edges: GraphEdge[],\n  ): void {\n    // Extract function call edges from exported functions and methods\n    for (const fn of sourceFile.getFunctions()) {\n      if (!this.isExported(fn)) continue;\n      const fnName = fn.getName();\n      if (!fnName) continue;\n\n      const fnSymbolId = this.buildSymbolId(filePath, fnName, 'function');\n\n      for (const call of fn.getDescendantsOfKind(SyntaxKind.CallExpression)) {\n        const calledName = call.getExpression().getText().split('.').pop();\n        if (!calledName || calledName === fnName) continue;\n\n        const resolved = this.resolveLocalCallTarget(sourceFile, filePath, calledName);\n        if (resolved) {\n          edges.push({ from: fnSymbolId, to: resolved, kind: 'calls' });\n        }\n      }\n\n      // GAP-11 FIX: constructor calls (new Foo())\n      for (const newExpr of fn.getDescendantsOfKind(SyntaxKind.NewExpression)) {\n        const calledName = newExpr.getExpression().getText().split('.').pop();\n        if (!calledName) continue;\n\n        const resolved = this.resolveLocalCallTarget(sourceFile, filePath, calledName);\n        if (resolved) {\n          edges.push({ from: fnSymbolId, to: resolved, kind: 'calls' });\n        }\n      }\n    }\n\n    // Extract calls from class methods\n    for (const cls of sourceFile.getClasses()) {\n      const className = cls.getName();\n      if (!className || !this.isExported(cls)) continue;\n\n      for (const method of cls.getMethods()) {\n        const methodName = method.getName();\n        const methodSymbolId = this.buildSymbolId(filePath, `${className}.${methodName}`, 'method');\n\n        for (const call of method.getDescendantsOfKind(SyntaxKind.CallExpression)) {\n          const calledText = call.getExpression().getText();\n          const calledName = calledText.split('.').pop();\n          if (!calledName || calledName === methodName) continue;\n\n          let resolved: string | undefined;\n          if (calledText.startsWith('this.')) {\n            resolved = this.resolveThisMethodCall(sourceFile, filePath, className, calledName);\n          } else {\n            resolved = this.resolveLocalCallTarget(sourceFile, filePath, calledName);\n          }\n          if (resolved) {\n            edges.push({ from: methodSymbolId, to: resolved, kind: 'calls' });\n          }\n        }\n\n        // GAP-11 FIX: constructor calls from methods (new Foo())\n        for (const newExpr of method.getDescendantsOfKind(SyntaxKind.NewExpression)) {\n          const calledText = newExpr.getExpression().getText();\n          const calledName = calledText.split('.').pop();\n          if (!calledName) continue;\n\n          let resolved: string | undefined;\n          if (calledText.startsWith('this.')) {\n            resolved = this.resolveThisMethodCall(sourceFile, filePath, className, calledName);\n          } else {\n            resolved = this.resolveLocalCallTarget(sourceFile, filePath, calledName);\n          }\n          if (resolved) {\n            edges.push({ from: methodSymbolId, to: resolved, kind: 'calls' });\n          }\n        }\n      }\n    }\n  }\n\n  private extractReferenceEdges(\n    sourceFile: SourceFile,\n    filePath: string,\n    edges: GraphEdge[],\n  ): void {\n    // Build map of all named imports from local modules: importedName → resolved symbolId\n    const importMap = new Map<string, string>();\n    for (const imp of sourceFile.getImportDeclarations()) {\n      const mod = imp.getModuleSpecifierValue();\n      if (!mod.startsWith('.') && !mod.startsWith('/')) continue;\n      const targetFile = this.resolveRelativeImport(filePath, mod);\n      for (const named of imp.getNamedImports()) {\n        importMap.set(named.getName(), this.resolveImportTarget(targetFile, named.getName()));\n      }\n      const defaultImport = imp.getDefaultImport();\n      if (defaultImport) {\n        importMap.set(defaultImport.getText(), this.resolveImportTarget(targetFile, defaultImport.getText()));\n      }\n    }\n    if (importMap.size === 0) return;\n\n    // Scan each exported symbol's body for identifier references to imports\n    for (const fn of sourceFile.getFunctions()) {\n      if (!this.isExported(fn)) continue;\n      const fnName = fn.getName();\n      if (!fnName) continue;\n      const fromId = this.buildSymbolId(filePath, fnName, 'function');\n      this.emitUsesEdges(fn, fromId, importMap, edges);\n    }\n\n    for (const cls of sourceFile.getClasses()) {\n      if (!this.isExported(cls)) continue;\n      const className = cls.getName();\n      if (!className) continue;\n\n      // Class-level references (property types, constructor params)\n      const classId = this.buildSymbolId(filePath, className, 'class');\n      this.emitUsesEdges(cls, classId, importMap, edges);\n    }\n  }\n\n  private emitUsesEdges(\n    node: Node,\n    fromId: string,\n    importMap: Map<string, string>,\n    edges: GraphEdge[],\n  ): void {\n    const seen = new Set<string>();\n    for (const id of node.getDescendantsOfKind(SyntaxKind.Identifier)) {\n      const name = id.getText();\n      if (seen.has(name)) continue;\n      const target = importMap.get(name);\n      if (target) {\n        seen.add(name);\n        edges.push({ from: fromId, to: target, kind: 'uses' });\n      }\n    }\n  }\n\n  private resolveLocalCallTarget(\n    sourceFile: SourceFile,\n    filePath: string,\n    calledName: string,\n  ): string | undefined {\n    // Check if the called name is imported from a local module\n    for (const imp of sourceFile.getImportDeclarations()) {\n      const moduleSpecifier = imp.getModuleSpecifierValue();\n      if (!moduleSpecifier.startsWith('.') && !moduleSpecifier.startsWith('/')) continue;\n\n      for (const named of imp.getNamedImports()) {\n        if (named.getName() === calledName) {\n          const targetFile = this.resolveRelativeImport(filePath, moduleSpecifier);\n          return this.resolveImportTarget(targetFile, calledName);\n        }\n      }\n    }\n\n    // Check if it's a locally defined function in the same file\n    for (const fn of sourceFile.getFunctions()) {\n      if (fn.getName() === calledName) {\n        return this.buildSymbolId(filePath, calledName, 'function');\n      }\n    }\n\n    return undefined;\n  }\n\n  private resolveThisMethodCall(\n    sourceFile: SourceFile,\n    filePath: string,\n    className: string,\n    calledName: string,\n  ): string | undefined {\n    for (const cls of sourceFile.getClasses()) {\n      if (cls.getName() !== className) continue;\n      for (const method of cls.getMethods()) {\n        if (method.getName() === calledName) {\n          return this.buildSymbolId(filePath, `${className}.${calledName}`, 'method');\n        }\n      }\n    }\n    return undefined;\n  }\n\n  // ── Helpers ─────────────────────────────────────────────────\n\n  private parseSource(filePath: string, source: string): SourceFile | undefined {\n    try {\n      const existing = this.project.getSourceFile(filePath);\n      if (existing && this.projectPreloaded) {\n        return existing;\n      }\n      if (existing) {\n        this.project.removeSourceFile(existing);\n      }\n      return this.project.createSourceFile(filePath, source, { overwrite: true });\n    } catch (err) {\n      console.error(`[ctxo:ts-morph] Parse failed for ${filePath}: ${(err as Error).message}`);\n      return undefined;\n    }\n  }\n\n  private cleanupSourceFile(filePath: string): void {\n    const existing = this.project.getSourceFile(filePath);\n    if (existing) {\n      this.project.removeSourceFile(existing);\n    }\n  }\n\n  private buildSymbolId(filePath: string, name: string, kind: SymbolKind): string {\n    return `${filePath}::${name}::${kind}`;\n  }\n\n  private resolveRelativeImport(fromFile: string, moduleSpecifier: string): string {\n    // Convert relative import like '../types.js' to project-relative 'src/core/types.ts'\n    const fromDir = dirname(fromFile);\n    let resolved = normalize(join(fromDir, moduleSpecifier)).replace(/\\\\/g, '/');\n\n    // Strip .js extension (TypeScript imports use .js but source files are .ts)\n    if (resolved.endsWith('.js')) {\n      resolved = resolved.slice(0, -3) + '.ts';\n    } else if (resolved.endsWith('.jsx')) {\n      resolved = resolved.slice(0, -4) + '.tsx';\n    } else if (!extname(resolved)) {\n      resolved += '.ts';\n    }\n\n    return resolved;\n  }\n\n  private resolveImportTarget(targetFile: string, name: string): string {\n    // BUG-8/9 FIX: check symbol registry first (populated from Phase 1 of indexing)\n    const prefix = `${targetFile}::${name}::`;\n    for (const kind of SYMBOL_KINDS) {\n      if (this.symbolRegistry.has(`${prefix}${kind}`)) {\n        return `${prefix}${kind}`;\n      }\n    }\n\n    // Try to find the symbol in the already-parsed project to get the correct kind\n    const targetSourceFile = this.project.getSourceFile(targetFile);\n    if (targetSourceFile) {\n      for (const fn of targetSourceFile.getFunctions()) {\n        if (fn.getName() === name && this.isExported(fn)) {\n          return this.buildSymbolId(targetFile, name, 'function');\n        }\n      }\n      for (const cls of targetSourceFile.getClasses()) {\n        if (cls.getName() === name && this.isExported(cls)) {\n          return this.buildSymbolId(targetFile, name, 'class');\n        }\n      }\n      for (const iface of targetSourceFile.getInterfaces()) {\n        if (iface.getName() === name && this.isExported(iface)) {\n          return this.buildSymbolId(targetFile, name, 'interface');\n        }\n      }\n      for (const t of targetSourceFile.getTypeAliases()) {\n        if (t.getName() === name && this.isExported(t)) {\n          return this.buildSymbolId(targetFile, name, 'type');\n        }\n      }\n    }\n    // Fallback: infer kind from naming conventions\n    const kind = this.inferSymbolKind(name);\n    return `${targetFile}::${name}::${kind}`;\n  }\n\n  private resolveSymbolReference(\n    sourceFile: SourceFile,\n    name: string,\n    defaultKind: SymbolKind,\n  ): string {\n    // Check if the name is imported\n    for (const imp of sourceFile.getImportDeclarations()) {\n      const moduleSpecifier = imp.getModuleSpecifierValue();\n      if (!moduleSpecifier.startsWith('.') && !moduleSpecifier.startsWith('/')) continue;\n\n      for (const named of imp.getNamedImports()) {\n        if (named.getName() === name) {\n          const resolved = imp.getModuleSpecifierSourceFile()?.getFilePath();\n          if (resolved) {\n            return `${this.normalizeFilePath(resolved)}::${name}::${defaultKind}`;\n          }\n          // Fallback: resolve relative module specifier manually\n          const sourceDir = dirname(this.normalizeFilePath(sourceFile.getFilePath()));\n          const resolvedPath = normalize(join(sourceDir, moduleSpecifier))\n            .replace(/\\\\/g, '/')\n            .replace(/\\.jsx$/, '.tsx')\n            .replace(/\\.js$/, '.ts');\n          return `${resolvedPath}::${name}::${defaultKind}`;\n        }\n      }\n    }\n\n    // Assume it's in the same file\n    return `${sourceFile.getFilePath()}::${name}::${defaultKind}`;\n  }\n\n  private inferSymbolKind(name: string): SymbolKind {\n    // Interface: starts with I followed by uppercase (IStoragePort, IGitPort)\n    if (/^I[A-Z]/.test(name) && name.length > 2) return 'interface';\n    // All caps with underscores: variable/constant (MAX_AMOUNT, EDGE_KINDS)\n    if (/^[A-Z][A-Z_0-9]+$/.test(name)) return 'variable';\n    // PascalCase: could be class, interface, or type — default to class\n    if (/^[A-Z]/.test(name)) return 'class';\n    // camelCase: function\n    return 'function';\n  }\n\n  private normalizeFilePath(filePath: string): string {\n    // Remove leading / from in-memory file system paths\n    return filePath.replace(/^\\//, '');\n  }\n\n  private getExportedSymbolIds(sourceFile: SourceFile, filePath: string): string[] {\n    const ids: string[] = [];\n    for (const fn of sourceFile.getFunctions()) {\n      if (!this.isExported(fn)) continue;\n      const name = fn.getName();\n      if (name) ids.push(this.buildSymbolId(filePath, name, 'function'));\n    }\n    for (const cls of sourceFile.getClasses()) {\n      if (!this.isExported(cls)) continue;\n      const name = cls.getName();\n      if (name) ids.push(this.buildSymbolId(filePath, name, 'class'));\n    }\n    for (const iface of sourceFile.getInterfaces()) {\n      if (!this.isExported(iface)) continue;\n      ids.push(this.buildSymbolId(filePath, iface.getName(), 'interface'));\n    }\n    for (const t of sourceFile.getTypeAliases()) {\n      if (!this.isExported(t)) continue;\n      ids.push(this.buildSymbolId(filePath, t.getName(), 'type'));\n    }\n    for (const stmt of sourceFile.getVariableStatements()) {\n      if (!this.isExported(stmt)) continue;\n      for (const decl of stmt.getDeclarations()) {\n        ids.push(this.buildSymbolId(filePath, decl.getName(), 'variable'));\n      }\n    }\n    return ids;\n  }\n\n  private isExported(node: Node): boolean {\n    if (Node.isExportable(node)) {\n      return node.isExported();\n    }\n    return false;\n  }\n\n  private countCyclomaticComplexity(node: FunctionDeclaration | MethodDeclaration): number {\n    let complexity = 1;\n\n    node.forEachDescendant((child) => {\n      switch (child.getKind()) {\n        case SyntaxKind.IfStatement:\n        case SyntaxKind.ConditionalExpression:\n        case SyntaxKind.ForStatement:\n        case SyntaxKind.ForInStatement:\n        case SyntaxKind.ForOfStatement:\n        case SyntaxKind.WhileStatement:\n        case SyntaxKind.DoStatement:\n        case SyntaxKind.CaseClause:\n        case SyntaxKind.CatchClause:\n        case SyntaxKind.BinaryExpression: {\n          const text = child.getText();\n          if (child.getKind() === SyntaxKind.BinaryExpression) {\n            if (text.includes('&&') || text.includes('||') || text.includes('??')) {\n              complexity++;\n            }\n          } else {\n            complexity++;\n          }\n          break;\n        }\n      }\n    });\n\n    return complexity;\n  }\n}\n","import { extname } from 'node:path';\nimport type { ILanguageAdapter } from '../../ports/i-language-adapter.js';\n\nexport class LanguageAdapterRegistry {\n  private readonly adaptersByExtension = new Map<string, ILanguageAdapter>();\n\n  register(adapter: ILanguageAdapter): void {\n    for (const ext of adapter.extensions) {\n      this.adaptersByExtension.set(ext.toLowerCase(), adapter);\n    }\n  }\n\n  getSupportedExtensions(): Set<string> {\n    return new Set(this.adaptersByExtension.keys());\n  }\n\n  getAdapter(filePath: string): ILanguageAdapter | undefined {\n    if (!filePath) return undefined;\n\n    const ext = extname(filePath).toLowerCase();\n    if (!ext) return undefined;\n\n    return this.adaptersByExtension.get(ext);\n  }\n}\n","import { writeFileSync, renameSync, mkdirSync, unlinkSync, existsSync } from 'node:fs';\nimport { dirname, join, resolve, sep } from 'node:path';\nimport type { FileIndex, CoChangeMatrix } from '../../core/types.js';\n\nexport class JsonIndexWriter {\n  private readonly indexDir: string;\n\n  constructor(ctxoRoot: string) {\n    this.indexDir = join(ctxoRoot, 'index');\n  }\n\n  write(fileIndex: FileIndex): void {\n    if (!fileIndex.file) {\n      throw new Error('FileIndex.file must not be empty');\n    }\n\n    const targetPath = this.resolveIndexPath(fileIndex.file);\n    mkdirSync(dirname(targetPath), { recursive: true });\n\n    const sorted = this.sortKeys(fileIndex);\n    const json = JSON.stringify(sorted, null, 2);\n    this.atomicWrite(targetPath, json);\n  }\n\n  writeCoChanges(matrix: CoChangeMatrix): void {\n    mkdirSync(this.indexDir, { recursive: true });\n    const targetPath = join(this.indexDir, 'co-changes.json');\n    this.atomicWrite(targetPath, JSON.stringify(matrix, null, 2));\n  }\n\n  private atomicWrite(targetPath: string, content: string): void {\n    const tmpPath = `${targetPath}.${process.pid}.tmp`;\n    writeFileSync(tmpPath, content, 'utf-8');\n    renameSync(tmpPath, targetPath);\n  }\n\n  delete(relativePath: string): void {\n    const targetPath = this.resolveIndexPath(relativePath);\n    if (existsSync(targetPath)) {\n      unlinkSync(targetPath);\n    }\n  }\n\n  private resolveIndexPath(relativePath: string): string {\n    const resolved = resolve(this.indexDir, `${relativePath}.json`);\n    const normalizedDir = resolve(this.indexDir) + sep;\n    if (!resolved.startsWith(normalizedDir)) {\n      throw new Error(`Path traversal detected: ${relativePath}`);\n    }\n    return resolved;\n  }\n\n  private sortKeys(obj: unknown): unknown {\n    if (Array.isArray(obj)) {\n      return obj.map((item) => this.sortKeys(item));\n    }\n    if (obj !== null && typeof obj === 'object') {\n      const sorted: Record<string, unknown> = {};\n      for (const key of Object.keys(obj).sort()) {\n        sorted[key] = this.sortKeys((obj as Record<string, unknown>)[key]);\n      }\n      return sorted;\n    }\n    return obj;\n  }\n}\n","import { readFileSync, writeFileSync, existsSync, mkdirSync } from 'node:fs';\nimport { join, dirname } from 'node:path';\n\nconst CURRENT_SCHEMA_VERSION = '1.0.0';\n\nexport class SchemaManager {\n  private readonly versionFilePath: string;\n\n  constructor(ctxoRoot: string) {\n    this.versionFilePath = join(ctxoRoot, 'index', 'schema-version');\n  }\n\n  currentVersion(): string {\n    return CURRENT_SCHEMA_VERSION;\n  }\n\n  readStoredVersion(): string | undefined {\n    if (!existsSync(this.versionFilePath)) {\n      return undefined;\n    }\n    return readFileSync(this.versionFilePath, 'utf-8').trim();\n  }\n\n  writeVersion(): void {\n    mkdirSync(dirname(this.versionFilePath), { recursive: true });\n    writeFileSync(this.versionFilePath, CURRENT_SCHEMA_VERSION, 'utf-8');\n  }\n\n  isCompatible(): boolean {\n    const stored = this.readStoredVersion();\n    if (!stored) return false;\n    return stored === CURRENT_SCHEMA_VERSION;\n  }\n}\n","import { join } from 'node:path';\nimport { SqliteStorageAdapter } from '../adapters/storage/sqlite-storage-adapter.js';\n\nexport class SyncCommand {\n  private readonly ctxoRoot: string;\n\n  constructor(projectRoot: string) {\n    this.ctxoRoot = join(projectRoot, '.ctxo');\n  }\n\n  async run(): Promise<void> {\n    console.error('[ctxo] Rebuilding SQLite cache from committed JSON index...');\n\n    const storage = new SqliteStorageAdapter(this.ctxoRoot);\n    try {\n      await storage.init();\n    } finally {\n      storage.close();\n    }\n\n    console.error('[ctxo] Sync complete');\n  }\n}\n","import { join } from 'node:path';\nimport { existsSync } from 'node:fs';\nimport { execFileSync } from 'node:child_process';\nimport { JsonIndexReader } from '../adapters/storage/json-index-reader.js';\nimport { SchemaManager } from '../adapters/storage/schema-manager.js';\n\nexport class StatusCommand {\n  private readonly projectRoot: string;\n  private readonly ctxoRoot: string;\n\n  constructor(projectRoot: string) {\n    this.projectRoot = projectRoot;\n    this.ctxoRoot = join(projectRoot, '.ctxo');\n  }\n\n  run(): void {\n    const indexDir = join(this.ctxoRoot, 'index');\n\n    if (!existsSync(indexDir)) {\n      console.error('[ctxo] No index found. Run \"ctxo index\" first.');\n      return;\n    }\n\n    const schemaManager = new SchemaManager(this.ctxoRoot);\n    const version = schemaManager.readStoredVersion() ?? 'unknown';\n\n    const reader = new JsonIndexReader(this.ctxoRoot);\n    const indices = reader.readAll();\n\n    const totalSymbols = indices.reduce((sum, idx) => sum + idx.symbols.length, 0);\n    const totalEdges = indices.reduce((sum, idx) => sum + idx.edges.length, 0);\n\n    console.error(`[ctxo] Index Status`);\n    console.error(`  Schema version: ${version}`);\n    console.error(`  Indexed files:  ${indices.length}`);\n    console.error(`  Total symbols:  ${totalSymbols}`);\n    console.error(`  Total edges:    ${totalEdges}`);\n\n    const cacheExists = existsSync(join(this.ctxoRoot, '.cache', 'symbols.db'));\n    console.error(`  SQLite cache:   ${cacheExists ? 'present' : 'missing (run ctxo sync)'}`);\n\n    // Per-file listing with timestamps\n    if (indices.length > 0) {\n      console.error('');\n      console.error('  Files:');\n\n      // Get source files to detect orphans\n      const sourceFiles = this.getSourceFiles();\n\n      for (const idx of indices.sort((a, b) => a.file.localeCompare(b.file))) {\n        const ts = new Date(idx.lastModified * 1000).toISOString();\n        const isOrphaned = sourceFiles.size > 0 && !sourceFiles.has(idx.file);\n        const badge = isOrphaned ? ' [orphaned]' : '';\n        console.error(`    ${idx.file}  ${ts}  (${idx.symbols.length} symbols, ${idx.edges.length} edges)${badge}`);\n      }\n    }\n  }\n\n  private getSourceFiles(): Set<string> {\n    try {\n      const output = execFileSync('git', ['ls-files', '--cached', '--others', '--exclude-standard'], {\n        cwd: this.projectRoot,\n        encoding: 'utf-8',\n      });\n      return new Set(output.split('\\n').map((l) => l.trim()).filter((l) => l.length > 0));\n    } catch {\n      return new Set();\n    }\n  }\n}\n","import { mkdtempSync, rmSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { tmpdir } from 'node:os';\nimport { IndexCommand } from './index-command.js';\nimport { JsonIndexReader } from '../adapters/storage/json-index-reader.js';\n\nexport class VerifyCommand {\n  private readonly projectRoot: string;\n\n  constructor(projectRoot: string) {\n    this.projectRoot = projectRoot;\n  }\n\n  async run(): Promise<void> {\n    console.error('[ctxo] Verifying index freshness...');\n\n    // Build index into a temp directory to avoid overwriting committed index\n    const tempDir = mkdtempSync(join(tmpdir(), 'ctxo-verify-'));\n\n    try {\n      const tempCtxo = join(tempDir, '.ctxo');\n\n      // Run index into temp .ctxo (does not touch committed index)\n      const indexCmd = new IndexCommand(this.projectRoot, tempCtxo);\n      await indexCmd.run({ skipSideEffects: true });\n\n      // Compare temp index with committed index\n      const committedReader = new JsonIndexReader(join(this.projectRoot, '.ctxo'));\n      const freshReader = new JsonIndexReader(tempCtxo);\n\n      const committedIndices = committedReader.readAll();\n      const freshIndices = freshReader.readAll();\n\n      // Compare full index: symbols + edges + intent + antiPatterns\n      const serialize = (i: { symbols: unknown; edges: unknown; intent: unknown; antiPatterns: unknown }) =>\n        JSON.stringify({ symbols: i.symbols, edges: i.edges, intent: i.intent, antiPatterns: i.antiPatterns });\n\n      const committedMap = new Map(committedIndices.map((i) => [i.file, serialize(i)]));\n      const freshMap = new Map(freshIndices.map((i) => [i.file, serialize(i)]));\n\n      let stale = false;\n\n      // Check for files that changed or were added\n      for (const [file, freshData] of freshMap) {\n        const committed = committedMap.get(file);\n        if (committed !== freshData) {\n          console.error(`[ctxo] STALE: ${file}`);\n          stale = true;\n        }\n      }\n\n      // Check for files that were removed\n      for (const file of committedMap.keys()) {\n        if (!freshMap.has(file)) {\n          console.error(`[ctxo] REMOVED: ${file}`);\n          stale = true;\n        }\n      }\n\n      if (stale) {\n        console.error('[ctxo] Index is STALE — run \"ctxo index\" and commit .ctxo/index/');\n        process.exit(1);\n      }\n\n      console.error('[ctxo] Index is up to date');\n    } finally {\n      rmSync(tempDir, { recursive: true, force: true });\n    }\n  }\n}\n","import { join } from 'node:path';\nimport { existsSync, readFileSync, writeFileSync, mkdirSync, chmodSync } from 'node:fs';\n\nconst CTXO_START = '# ctxo-start';\nconst CTXO_END = '# ctxo-end';\n\nconst POST_COMMIT_CONTENT = `\n${CTXO_START}\n# Incremental re-index on commit (only changed files)\nif command -v ctxo >/dev/null 2>&1; then\n  for file in $(git diff --name-only HEAD~1 HEAD 2>/dev/null); do\n    ctxo index --file \"$file\" 2>/dev/null || true\n  done\nfi\n${CTXO_END}\n`.trim();\n\nconst POST_MERGE_CONTENT = `\n${CTXO_START}\n# Rebuild SQLite cache after merge (index updated via git pull)\nif command -v ctxo >/dev/null 2>&1; then\n  ctxo sync 2>/dev/null || true\nfi\n${CTXO_END}\n`.trim();\n\nexport class InitCommand {\n  private readonly projectRoot: string;\n\n  constructor(projectRoot: string) {\n    this.projectRoot = projectRoot;\n  }\n\n  run(): void {\n    const hooksDir = join(this.projectRoot, '.git', 'hooks');\n\n    if (!existsSync(join(this.projectRoot, '.git'))) {\n      console.error('[ctxo] Not a git repository. Run \"git init\" first.');\n      process.exit(1);\n    }\n\n    mkdirSync(hooksDir, { recursive: true });\n\n    this.installHook(hooksDir, 'post-commit', POST_COMMIT_CONTENT);\n    this.installHook(hooksDir, 'post-merge', POST_MERGE_CONTENT);\n\n    console.error('[ctxo] Git hooks installed (post-commit, post-merge)');\n  }\n\n  private installHook(hooksDir: string, hookName: string, hookContent: string): void {\n    const hookPath = join(hooksDir, hookName);\n\n    let existing = '';\n    if (existsSync(hookPath)) {\n      existing = readFileSync(hookPath, 'utf-8');\n\n      // Already installed — idempotent\n      if (existing.includes(CTXO_START)) {\n        console.error(`[ctxo] ${hookName} hook already has ctxo block — skipping`);\n        return;\n      }\n    } else {\n      existing = '#!/bin/sh\\n';\n    }\n\n    // Append ctxo block\n    const updated = existing.endsWith('\\n')\n      ? existing + '\\n' + hookContent + '\\n'\n      : existing + '\\n\\n' + hookContent + '\\n';\n\n    writeFileSync(hookPath, updated, 'utf-8');\n    chmodSync(hookPath, 0o755);\n  }\n}\n","import { join, extname, relative } from 'node:path';\nimport { readFileSync } from 'node:fs';\nimport { TsMorphAdapter } from '../adapters/language/ts-morph-adapter.js';\nimport { LanguageAdapterRegistry } from '../adapters/language/language-adapter-registry.js';\nimport { JsonIndexWriter } from '../adapters/storage/json-index-writer.js';\nimport { SqliteStorageAdapter } from '../adapters/storage/sqlite-storage-adapter.js';\nimport { ChokidarWatcherAdapter } from '../adapters/watcher/chokidar-watcher-adapter.js';\nimport { ContentHasher } from '../core/staleness/content-hasher.js';\nimport { SimpleGitAdapter } from '../adapters/git/simple-git-adapter.js';\nimport { RevertDetector } from '../core/why-context/revert-detector.js';\nimport type { FileIndex, CommitIntent, AntiPattern } from '../core/types.js';\n\nconst DEBOUNCE_MS = 300;\n\nexport class WatchCommand {\n  private readonly projectRoot: string;\n  private readonly ctxoRoot: string;\n\n  constructor(projectRoot: string) {\n    this.projectRoot = projectRoot;\n    this.ctxoRoot = join(projectRoot, '.ctxo');\n  }\n\n  async run(): Promise<void> {\n    console.error('[ctxo] Starting file watcher...');\n\n    const registry = new LanguageAdapterRegistry();\n    registry.register(new TsMorphAdapter());\n    this.registerTreeSitterAdapters(registry);\n    const supportedExtensions = registry.getSupportedExtensions();\n\n    const writer = new JsonIndexWriter(this.ctxoRoot);\n    const storage = new SqliteStorageAdapter(this.ctxoRoot);\n    await storage.init();\n    const hasher = new ContentHasher();\n\n    const gitAdapter = new SimpleGitAdapter(this.projectRoot);\n    const revertDetector = new RevertDetector();\n    const watcher = new ChokidarWatcherAdapter(this.projectRoot);\n    const pendingFiles = new Map<string, NodeJS.Timeout>();\n\n    const reindexFile = async (filePath: string) => {\n      const adapter = registry.getAdapter(filePath);\n      if (!adapter) return;\n\n      const relativePath = relative(this.projectRoot, filePath).replace(/\\\\/g, '/');\n\n      try {\n        const source = readFileSync(filePath, 'utf-8');\n        const lastModified = Math.floor(Date.now() / 1000);\n\n        const symbols = adapter.extractSymbols(relativePath, source);\n        const edges = adapter.extractEdges(relativePath, source);\n        const complexity = adapter.extractComplexity(relativePath, source);\n\n        // Git history and anti-patterns\n        const commits = await gitAdapter.getCommitHistory(relativePath);\n        const intent: CommitIntent[] = commits.map((c) => ({\n          hash: c.hash, message: c.message, date: c.date, kind: 'commit' as const,\n        }));\n        const antiPatterns: AntiPattern[] = revertDetector.detect(commits);\n\n        const fileIndex: FileIndex = {\n          file: relativePath,\n          lastModified,\n          contentHash: hasher.hash(source),\n          symbols,\n          edges,\n          complexity,\n          intent,\n          antiPatterns,\n        };\n\n        writer.write(fileIndex);\n        storage.writeSymbolFile(fileIndex);\n        console.error(`[ctxo] Re-indexed: ${relativePath}`);\n      } catch (err) {\n        console.error(`[ctxo] Failed to re-index ${relativePath}: ${(err as Error).message}`);\n      }\n    };\n\n    const debouncedReindex = (filePath: string) => {\n      const existing = pendingFiles.get(filePath);\n      if (existing) clearTimeout(existing);\n\n      pendingFiles.set(\n        filePath,\n        setTimeout(() => {\n          pendingFiles.delete(filePath);\n          reindexFile(filePath);\n        }, DEBOUNCE_MS),\n      );\n    };\n\n    watcher.start((event, filePath) => {\n      if (event === 'unlink') {\n        const ext = extname(filePath).toLowerCase();\n        if (!supportedExtensions.has(ext)) return;\n\n        const relativePath = relative(this.projectRoot, filePath).replace(/\\\\/g, '/');\n        writer.delete(relativePath);\n        storage.deleteSymbolFile(relativePath);\n        console.error(`[ctxo] Removed from index: ${relativePath}`);\n      } else {\n        debouncedReindex(filePath);\n      }\n    });\n\n    console.error('[ctxo] Watching for file changes... (Ctrl+C to stop)');\n\n    const cleanup = () => {\n      console.error('\\n[ctxo] Stopping watcher...');\n      for (const timeout of pendingFiles.values()) {\n        clearTimeout(timeout);\n      }\n      watcher.stop().then(() => {\n        storage.close();\n        console.error('[ctxo] Watcher stopped');\n        process.exit(0);\n      });\n    };\n\n    process.on('SIGINT', cleanup);\n    process.on('SIGTERM', cleanup);\n  }\n\n  private registerTreeSitterAdapters(registry: LanguageAdapterRegistry): void {\n    try {\n      // eslint-disable-next-line @typescript-eslint/no-require-imports\n      const { GoAdapter } = require('../adapters/language/go-adapter.js');\n      registry.register(new GoAdapter());\n    } catch {\n      console.error('[ctxo] Go adapter unavailable (tree-sitter-go not installed)');\n    }\n    try {\n      // eslint-disable-next-line @typescript-eslint/no-require-imports\n      const { CSharpAdapter } = require('../adapters/language/csharp-adapter.js');\n      registry.register(new CSharpAdapter());\n    } catch {\n      console.error('[ctxo] C# adapter unavailable (tree-sitter-c-sharp not installed)');\n    }\n  }\n}\n","import { watch, type FSWatcher } from 'chokidar';\nimport type { IWatcherPort, FileChangeHandler } from '../../ports/i-watcher-port.js';\n\nconst DEFAULT_IGNORED = [\n  '**/node_modules/**',\n  '**/.git/**',\n  '**/.ctxo/**',\n  '**/dist/**',\n  '**/coverage/**',\n];\n\nexport class ChokidarWatcherAdapter implements IWatcherPort {\n  private readonly projectRoot: string;\n  private readonly ignored: string[];\n  private watcher: FSWatcher | undefined;\n\n  constructor(projectRoot: string, ignored?: string[]) {\n    this.projectRoot = projectRoot;\n    this.ignored = ignored ?? DEFAULT_IGNORED;\n  }\n\n  start(handler: FileChangeHandler): void {\n    if (this.watcher) {\n      throw new Error('Watcher already started. Call stop() before starting again.');\n    }\n\n    this.watcher = watch(this.projectRoot, {\n      ignored: this.ignored,\n      persistent: true,\n      ignoreInitial: true,\n    });\n\n    this.watcher.on('add', (path) => handler('add', path));\n    this.watcher.on('change', (path) => handler('change', path));\n    this.watcher.on('unlink', (path) => handler('unlink', path));\n  }\n\n  async stop(): Promise<void> {\n    if (this.watcher) {\n      await this.watcher.close();\n      this.watcher = undefined;\n    }\n  }\n}\n","import { IndexCommand } from './index-command.js';\nimport { SyncCommand } from './sync-command.js';\nimport { StatusCommand } from './status-command.js';\nimport { VerifyCommand } from './verify-command.js';\nimport { InitCommand } from './init-command.js';\nimport { WatchCommand } from './watch-command.js';\n\nexport class CliRouter {\n  private readonly projectRoot: string;\n\n  constructor(projectRoot: string) {\n    this.projectRoot = projectRoot;\n  }\n\n  async route(args: string[]): Promise<void> {\n    const command = args[0];\n\n    if (!command || command === '--help' || command === '-h') {\n      this.printHelp();\n      return;\n    }\n\n    switch (command) {\n      case 'index': {\n        const fileIdx = args.indexOf('--file');\n        const fileArg = fileIdx !== -1 ? args[fileIdx + 1] : undefined;\n        if (fileIdx !== -1 && (!fileArg || fileArg.startsWith('--'))) {\n          console.error('[ctxo] --file requires a path argument');\n          process.exit(1);\n          return;\n        }\n        const checkArg = args.includes('--check');\n        const skipHistory = args.includes('--skip-history');\n        const maxHistoryIdx = args.indexOf('--max-history');\n        const maxHistoryArg = maxHistoryIdx !== -1 ? Number(args[maxHistoryIdx + 1]) : undefined;\n        if (maxHistoryIdx !== -1 && (!maxHistoryArg || isNaN(maxHistoryArg) || maxHistoryArg < 1)) {\n          console.error('[ctxo] --max-history requires a positive integer');\n          process.exit(1);\n          return;\n        }\n        await new IndexCommand(this.projectRoot).run({ file: fileArg, check: checkArg, skipHistory, maxHistory: maxHistoryArg });\n        break;\n      }\n\n      case 'sync':\n        await new SyncCommand(this.projectRoot).run();\n        break;\n\n      case 'watch':\n        await new WatchCommand(this.projectRoot).run();\n        break;\n\n      case 'verify-index':\n        await new VerifyCommand(this.projectRoot).run();\n        break;\n\n      case 'status':\n        new StatusCommand(this.projectRoot).run();\n        break;\n\n      case 'init':\n        new InitCommand(this.projectRoot).run();\n        break;\n\n      default:\n        console.error(`[ctxo] Unknown command: \"${command}\". Run \"ctxo --help\" for usage.`);\n        process.exit(1);\n        return;\n    }\n  }\n\n  private printHelp(): void {\n    console.error(`\nctxo — MCP server for dependency-aware codebase context\n\nUsage:\n  ctxo                      Start MCP server (stdio transport)\n  ctxo index                Build full codebase index (--max-history N, default 20)\n  ctxo sync                 Rebuild SQLite cache from committed JSON index\n  ctxo watch                Start file watcher for incremental re-indexing\n  ctxo verify-index         CI gate: fail if index is stale\n  ctxo status               Show index manifest\n  ctxo init                 Install git hooks\n  ctxo --help               Show this help message\n`.trim());\n  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