@ctxo/cli 0.10.0 → 0.11.0

package/dist/json-index-reader-UYS74USB.js

@@ -0,0 +1,9 @@
+#!/usr/bin/env node
+import {
+  JsonIndexReader
+} from "./chunk-CDGQGCVN.js";
+import "./chunk-5DSKZJNN.js";
+export {
+  JsonIndexReader
+};
+//# sourceMappingURL=json-index-reader-UYS74USB.js.map

package/llms-full.txt

@@ -22,13 +22,14 @@ MCP client configuration:
 
 ## Monorepo & Plugin Architecture (v0.7+)
 
-Ctxo is a pnpm workspace monorepo with five packages:
+Ctxo is a pnpm workspace monorepo with six packages:
 
 - `@ctxo/cli` (packages/cli) — CLI entry, composition root, MCP server, tool handlers
 - `@ctxo/plugin-api` (packages/plugin-api) — `CtxoLanguagePlugin` v1 protocol interface
 - `@ctxo/lang-typescript` — ts-morph (full tier) plugin for TS/JS
 - `@ctxo/lang-go` — tree-sitter / gopls plugin for Go
 - `@ctxo/lang-csharp` — Roslyn plugin for C#
+- `@ctxo/lang-java` - tree-sitter Java plugin (syntax tier); full tier via `@ctxo/lang-java-analyzer` companion package (JRE 17+ required)
 
 Plugin protocol v1 (`CtxoLanguagePlugin`):
 - `apiVersion: 1`

package/llms.txt

@@ -20,6 +20,7 @@ ctxo                       # Start MCP server (stdio)
 - `@ctxo/lang-typescript` — ts-morph full-tier plugin
 - `@ctxo/lang-go` — tree-sitter / gopls plugin
 - `@ctxo/lang-csharp` — Roslyn plugin
+- `@ctxo/lang-java` - tree-sitter Java plugin (syntax tier built-in; full tier via `@ctxo/lang-java-analyzer` companion, requires JRE 17+)
 
 Language adapters ship as separate npm packages and are discovered by scanning the project `package.json` for `@ctxo/lang-*` or `ctxo-lang-*` dependencies.
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ctxo/cli",
-  "version": "0.10.0",
+  "version": "0.11.0",
   "description": "MCP server delivering dependency-aware, history-enriched context for codebases",
   "type": "module",
   "engines": {
@@ -40,7 +40,7 @@
     "sql.js": "^1.14.1",
     "yaml": "^2.6.1",
     "zod": "^4.3.6",
-    "@ctxo/plugin-api": "0.7.1"
+    "@ctxo/plugin-api": "0.7.2"
   },
   "devDependencies": {
     "@types/node": "^22.15.3",
@@ -52,9 +52,9 @@
     "typescript": "^5.8.3",
     "typescript-eslint": "^8.57.2",
     "vitest": "^3.1.3",
-    "@ctxo/lang-typescript": "0.7.1",
+    "@ctxo/lang-csharp": "0.7.3",
     "@ctxo/lang-go": "0.8.0",
-    "@ctxo/lang-csharp": "0.7.2"
+    "@ctxo/lang-typescript": "0.7.1"
   },
   "repository": {
     "type": "git",

package/dist/chunk-2TVHKCCU.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/adapters/storage/json-index-reader.ts","../src/core/types.ts"],"sourcesContent":["import { readFileSync, readdirSync, existsSync, realpathSync } from 'node:fs';\nimport { join, relative } from 'node:path';\nimport { FileIndexSchema, type FileIndex } from '../../core/types.js';\n\nexport class JsonIndexReader {\n  private readonly indexDir: string;\n\n  constructor(ctxoRoot: string) {\n    this.indexDir = join(ctxoRoot, 'index');\n  }\n\n  readAll(): FileIndex[] {\n    if (!existsSync(this.indexDir)) {\n      return [];\n    }\n\n    const jsonFiles = this.collectJsonFiles(this.indexDir);\n    const results: FileIndex[] = [];\n\n    for (const filePath of jsonFiles) {\n      const parsed = this.readSingle(filePath);\n      if (parsed) {\n        results.push(parsed);\n      }\n    }\n\n    return results;\n  }\n\n  readSingle(absolutePath: string): FileIndex | undefined {\n    try {\n      const raw = readFileSync(absolutePath, 'utf-8');\n      const data: unknown = JSON.parse(raw);\n      const result = FileIndexSchema.safeParse(data);\n\n      if (!result.success) {\n        const rel = relative(this.indexDir, absolutePath);\n        console.error(\n          `[ctxo:json-reader] Invalid schema in ${rel}: ${result.error.message}`,\n        );\n        return undefined;\n      }\n\n      return result.data;\n    } catch (err) {\n      const rel = relative(this.indexDir, absolutePath);\n      console.error(\n        `[ctxo:json-reader] Failed to read ${rel}: ${(err as Error).message}`,\n      );\n      return undefined;\n    }\n  }\n\n  private collectJsonFiles(dir: string, visited: Set<string> = new Set()): string[] {\n    const realDir = realpathSync(dir);\n    if (visited.has(realDir)) return []; // Guard against symlink loops\n    visited.add(realDir);\n\n    const files: string[] = [];\n\n    for (const entry of readdirSync(dir, { withFileTypes: true })) {\n      if (entry.isSymbolicLink()) continue; // Skip symlinks 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──────────────────────────────────────────────────\n\nexport const EDGE_KINDS = [\n  'imports',\n  'calls',\n  'extends',\n  'implements',\n  'uses',\n] as const;\n\nexport const EdgeKindSchema = z.enum(EDGE_KINDS);\nexport type EdgeKind = z.infer<typeof EdgeKindSchema>;\n\n// ── Detail Levels ───────────────────────────────────────────────\n\nexport const DETAIL_LEVELS = [1, 2, 3, 4] as const;\n\nexport const DetailLevelSchema = z.union([\n  z.literal(1),\n  z.literal(2),\n  z.literal(3),\n  z.literal(4),\n]);\nexport type DetailLevel = z.infer<typeof DetailLevelSchema>;\n\n// ── Symbol ID ───────────────────────────────────────────────────\n\n/**\n * Format: \"<relativeFile>::<name>::<kind>\"\n * Example: \"src/foo.ts::myFn::function\"\n */\nexport const SymbolIdSchema = z\n  .string()\n  .min(1)\n  .refine(\n    (value) => {\n      const parts = value.split('::');\n      if (parts.length !== 3) return false;\n      const [file, name, kind] = parts;\n      if (!file || !name || !kind) return false;\n      return SymbolKindSchema.safeParse(kind).success;\n    },\n    { message: 'Symbol ID must match format \"<file>::<name>::<kind>\"' },\n  );\nexport type SymbolId = z.infer<typeof SymbolIdSchema>;\n\n// ── Symbol Node ─────────────────────────────────────────────────\n\nexport const SymbolNodeSchema = z\n  .object({\n    symbolId: SymbolIdSchema,\n    name: z.string().min(1),\n    kind: SymbolKindSchema,\n    startLine: z.number().int().nonnegative(),\n    endLine: z.number().int().nonnegative(),\n    startOffset: z.number().int().nonnegative().optional(),\n    endOffset: z.number().int().nonnegative().optional(),\n  })\n  .refine((node) => node.endLine >= node.startLine, {\n    message: 'endLine must be >= startLine',\n  });\nexport type SymbolNode = z.infer<typeof SymbolNodeSchema>;\n\n// ── Graph Edge ──────────────────────────────────────────────────\n\nexport const GraphEdgeSchema = z.object({\n  from: SymbolIdSchema,\n  to: SymbolIdSchema,\n  kind: EdgeKindSchema,\n  typeOnly: z.boolean().optional(),\n});\nexport type GraphEdge = z.infer<typeof GraphEdgeSchema>;\n\n// ── Commit Intent ───────────────────────────────────────────────\n\nexport const CommitIntentSchema = z.object({\n  hash: z.string().min(1),\n  message: z.string(),\n  date: z.string().min(1),\n  kind: z.literal('commit'),\n});\nexport type CommitIntent = z.infer<typeof CommitIntentSchema>;\n\n// ── Anti-Pattern ────────────────────────────────────────────────\n\nexport const AntiPatternSchema = z.object({\n  hash: z.string().min(1),\n  message: z.string(),\n  date: z.string().min(1),\n});\nexport type AntiPattern = z.infer<typeof AntiPatternSchema>;\n\n// ── File Index ──────────────────────────────────────────────────\n\nexport const ComplexityMetricsSchema = z.object({\n  symbolId: z.string().min(1),\n  cyclomatic: z.number().nonnegative(),\n});\n\nexport const FileIndexSchema = z.object({\n  file: z.string().min(1),\n  lastModified: z.number().nonnegative(),\n  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TruncationInfo;\n}\n\n// ── Complexity & Churn ──────────────────────────────────────────\n\nexport interface ComplexityMetrics {\n  readonly symbolId: string;\n  readonly cyclomatic: number;\n}\n\nexport interface ChurnData {\n  readonly filePath: string;\n  readonly commitCount: number;\n}\n\nexport const SCORE_BANDS = ['low', 'medium', 'high'] as const;\nexport type ScoreBand = (typeof SCORE_BANDS)[number];\n\nexport interface ChangeIntelligenceScore {\n  readonly symbolId: string;\n  readonly complexity: number;\n  readonly churn: number;\n  readonly composite: number;\n  readonly band: ScoreBand;\n}\n\n// ── Why-Context Result ──────────────────────────────────────────\n\nexport interface WhyContextResult {\n  readonly commitHistory: readonly CommitIntent[];\n  readonly antiPatternWarnings: readonly AntiPattern[];\n  readonly changeIntelligence?: ChangeIntelligenceScore;\n}\n\n// ── Co-Change Analysis ─────────────────────────────────────────\n\nexport interface CoChangeEntry {\n  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edgeKind: EdgeKind;\n  readonly historicalEdgesBetweenClusters: number;\n  readonly severity: 'high' | 'medium';\n}\n\n// ── Persisted architectural artifacts ──────────────────────────\n// Written by `ctxo index` next to communities.json so the static\n// HTML visualizer can render Architecture views without re-running\n// detectors in the browser.\n\nexport type ConfidenceLevel = 'high' | 'medium' | 'low';\n\nexport interface DriftEventsArtifact {\n  readonly version: 1;\n  readonly computedAt: string;\n  readonly commitSha: string;\n  readonly confidence: ConfidenceLevel;\n  readonly snapshotsAvailable: number;\n  readonly hint?: string;\n  readonly events: readonly DriftEvent[];\n}\n\nexport interface BoundaryViolationsArtifact {\n  readonly version: 1;\n  readonly computedAt: string;\n  readonly commitSha: string;\n  readonly confidence: ConfidenceLevel;\n  readonly snapshotsAvailable: number;\n  readonly hint?: string;\n  readonly violations: readonly 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package/dist/chunk-6EKERTJ7.js.map

@@ -1 +0,0 @@
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package/dist/chunk-I6HLEK4G.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/adapters/storage/sqlite-storage-adapter.ts","../src/adapters/storage/community-snapshot-writer.ts","../src/adapters/git/simple-git-adapter.ts","../src/adapters/stats/session-recorder-adapter.ts","../src/adapters/workspace/single-package-workspace.ts","../src/core/config/load-config.ts","../src/core/config/config-schema.ts","../src/core/graph/symbol-graph.ts","../src/core/why-context/revert-detector.ts","../src/core/overlay/drift-detector.ts","../src/core/blast-radius/blast-radius-calculator.ts","../src/core/overlay/architectural-overlay.ts","../src/core/dead-code/dead-code-detector.ts","../src/core/importance/pagerank-calculator.ts","../src/core/overlay/boundary-violation-detector.ts","../src/core/co-change/co-change-analyzer.ts"],"sourcesContent":["import initSqlJs, { type Database } from 'sql.js';\nimport { readFileSync, writeFileSync, existsSync, mkdirSync } from 'node:fs';\nimport { join, dirname } from 'node:path';\nimport type {\n  CommunitySnapshot,\n  FileIndex,\n  GraphEdge,\n  SymbolNode,\n} from '../../core/types.js';\nimport type { IStoragePort } from '../../ports/i-storage-port.js';\nimport { CommunitySnapshotWriter } from './community-snapshot-writer.js';\nimport { JsonIndexReader } from './json-index-reader.js';\nimport { createLogger } from '../../core/logger.js';\n\nconst log = createLogger('ctxo:storage');\n\nexport interface SqliteStorageAdapterOptions {\n  /**\n   * Acknowledge writes to a production (non-tmpdir) `.ctxo/` root. Required\n   * when the CLI talks to the user's real project. Tests using mkdtempSync\n   * paths can omit this; they are auto-recognised as safe.\n   */\n  readonly allowProductionPath?: boolean;\n}\n\nexport class SqliteStorageAdapter implements IStoragePort {\n  private db: Database | undefined;\n  private readonly dbPath: string;\n  private readonly ctxoRoot: string;\n  private readonly communityWriter: CommunitySnapshotWriter;\n\n  constructor(ctxoRoot: string, options: SqliteStorageAdapterOptions = {}) {\n    this.ctxoRoot = ctxoRoot;\n    this.dbPath = join(ctxoRoot, '.cache', 'symbols.db');\n    this.communityWriter = new CommunitySnapshotWriter(ctxoRoot, {\n      allowProductionPath: options.allowProductionPath,\n    });\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    if (existsSync(this.dbPath)) {\n      try {\n        const buffer = readFileSync(this.dbPath);\n        this.db = new SQL.Database(buffer);\n      } catch {\n        this.db = new SQL.Database();\n      }\n    } else {\n      this.db = new SQL.Database();\n    }\n    this.createTables();\n    this.clearIndexTables();\n  }\n\n  /** Returns the underlying sql.js Database instance. Throws if not initialized. */\n  getDb(): Database {\n    if (!this.db) {\n      throw new Error('SqliteStorageAdapter not initialized. Call init() first.');\n    }\n    return this.db;\n  }\n\n  private database(): Database {\n    return this.getDb();\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 clearIndexTables(): void {\n    const db = this.database();\n    db.run('DELETE FROM edges');\n    db.run('DELETE FROM symbols');\n    db.run('DELETE FROM files');\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  readCommunities(): CommunitySnapshot | undefined {\n    return this.communityWriter.readCurrent();\n  }\n\n  writeCommunities(snapshot: CommunitySnapshot): void {\n    this.communityWriter.writeSnapshot(snapshot);\n  }\n\n  listCommunityHistory(limit?: number): CommunitySnapshot[] {\n    return this.communityWriter.listHistory(limit);\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 {\n  existsSync,\n  mkdirSync,\n  readFileSync,\n  readdirSync,\n  unlinkSync,\n} from 'node:fs';\nimport { tmpdir } from 'node:os';\nimport { basename, join, resolve } from 'node:path';\n\nimport { createLogger } from '../../core/logger.js';\nimport type { CommunitySnapshot } from '../../core/types.js';\nimport { atomicWrite } from './atomic-write.js';\n\nconst log = createLogger('ctxo:community-snapshot');\n\nconst DEFAULT_HISTORY_LIMIT = 10;\nconst HISTORY_DIR_NAME = 'communities.history';\nconst CURRENT_FILE_NAME = 'communities.json';\nconst NOCOMMIT_SHA = 'nocommit';\n\nexport interface CommunitySnapshotWriterOptions {\n  readonly historyLimit?: number;\n  /**\n   * Acknowledge that this writer targets a production `.ctxo/` root (user's\n   * real project). Required when the path is outside the system tmpdir; this\n   * prevents test runs from accidentally writing a tiny/invalid snapshot into\n   * the developer's real project via an unisolated fixture.\n   */\n  readonly allowProductionPath?: boolean;\n}\n\nexport class CommunitySnapshotWriter {\n  private readonly indexDir: string;\n  private readonly historyDir: string;\n  private readonly historyLimit: number;\n\n  constructor(\n    ctxoRoot: string,\n    historyLimitOrOptions: number | CommunitySnapshotWriterOptions = DEFAULT_HISTORY_LIMIT,\n  ) {\n    const options: CommunitySnapshotWriterOptions =\n      typeof historyLimitOrOptions === 'number'\n        ? { historyLimit: historyLimitOrOptions }\n        : historyLimitOrOptions;\n\n    this.indexDir = join(ctxoRoot, 'index');\n    this.historyDir = join(this.indexDir, HISTORY_DIR_NAME);\n    this.historyLimit = options.historyLimit ?? DEFAULT_HISTORY_LIMIT;\n\n    assertSafeWritePath(ctxoRoot, options.allowProductionPath ?? false);\n  }\n\n  writeSnapshot(snapshot: CommunitySnapshot): void {\n    mkdirSync(this.indexDir, { recursive: true });\n    mkdirSync(this.historyDir, { recursive: true });\n\n    // Archive the previous current snapshot (if any) into history BEFORE\n    // overwriting. This keeps history as \"snapshots older than current\" —\n    // drift and boundary-violation detectors compare current vs history[0]\n    // and must not see current in both positions.\n    //\n    // Skip archival for snapshots whose commitSha is 'nocommit' (git\n    // unavailable at write time). They have no stable anchor for drift\n    // comparison and would pollute history with indistinguishable entries.\n    const currentPath = join(this.indexDir, CURRENT_FILE_NAME);\n    if (existsSync(currentPath)) {\n      try {\n        const existingRaw = readFileSync(currentPath, 'utf-8');\n        const existing = JSON.parse(existingRaw) as CommunitySnapshot;\n        if (existing.commitSha && existing.commitSha !== NOCOMMIT_SHA) {\n          const historyFile = this.historyFilename(existing);\n          this.atomicWrite(join(this.historyDir, historyFile), existingRaw);\n        }\n      } catch (err) {\n        log.error(`failed to archive existing snapshot: ${(err as Error).message}`);\n      }\n    }\n\n    const json = JSON.stringify(snapshot, null, 2);\n    this.atomicWrite(currentPath, json);\n\n    this.rotateHistory();\n  }\n\n  readCurrent(): CommunitySnapshot | undefined {\n    const path = join(this.indexDir, CURRENT_FILE_NAME);\n    if (!existsSync(path)) return undefined;\n    return this.safeParse(path);\n  }\n\n  listHistory(limit?: number): CommunitySnapshot[] {\n    if (!existsSync(this.historyDir)) return [];\n    const entries = readdirSync(this.historyDir)\n      .filter((name) => name.endsWith('.json'))\n      .sort()\n      .reverse();\n    const snapshots: CommunitySnapshot[] = [];\n    for (const name of entries) {\n      const snap = this.safeParse(join(this.historyDir, name));\n      if (!snap) continue;\n      // Defense in depth: filter any legacy `nocommit` entries that slipped\n      // into history before the writer skip-archival guard landed.\n      if (!snap.commitSha || snap.commitSha === NOCOMMIT_SHA) continue;\n      snapshots.push(snap);\n      if (typeof limit === 'number' && snapshots.length >= limit) break;\n    }\n    return snapshots;\n  }\n\n  private atomicWrite(targetPath: string, content: string): void {\n    atomicWrite(targetPath, content);\n  }\n\n  private historyFilename(snapshot: CommunitySnapshot): string {\n    const ts = snapshot.computedAt.replace(/[:.]/g, '-');\n    const sha = snapshot.commitSha || 'nocommit';\n    const base = join(this.historyDir, `${ts}-${sha}`);\n    // Collision guard: if the same-timestamp file already exists (rare but\n    // possible with sub-millisecond writes), append a monotonic suffix.\n    let candidate = `${base}.json`;\n    let n = 1;\n    while (existsSync(candidate)) {\n      candidate = `${base}.${n++}.json`;\n      if (n > 1_000) break; // safety\n    }\n    return candidate.slice(this.historyDir.length + 1);\n  }\n\n  private rotateHistory(): void {\n    if (!existsSync(this.historyDir)) return;\n    const entries = readdirSync(this.historyDir)\n      .filter((name) => name.endsWith('.json'))\n      .sort();\n    const excess = entries.length - this.historyLimit;\n    if (excess <= 0) return;\n    for (let i = 0; i < excess; i++) {\n      const target = join(this.historyDir, entries[i]!);\n      try {\n        unlinkSync(target);\n      } catch (err) {\n        log.error(`failed to rotate ${basename(target)}: ${(err as Error).message}`);\n      }\n    }\n  }\n\n  private safeParse(path: string): CommunitySnapshot | undefined {\n    try {\n      const raw = readFileSync(path, 'utf-8');\n      return JSON.parse(raw) as CommunitySnapshot;\n    } catch (err) {\n      log.error(`failed to parse ${basename(path)}: ${(err as Error).message}`);\n      return undefined;\n    }\n  }\n}\n\n/**\n * Production `.ctxo/` roots must be opted into explicitly. This catches\n * the rogue case where a test forgets to pass a tmpdir and would otherwise\n * clobber the developer's real snapshot (as happened during v0.8 runtime\n * analysis — a 39-node modularity-0 snapshot appeared in the repo root from\n * an unisolated fixture).\n */\nfunction assertSafeWritePath(ctxoRoot: string, allowProduction: boolean): void {\n  const resolved = resolve(ctxoRoot);\n  const tmpRoot = resolve(tmpdir());\n  const inTmp = resolved.startsWith(tmpRoot);\n  if (inTmp || allowProduction) return;\n  throw new Error(\n    `CommunitySnapshotWriter: refusing to write to non-tmp path ${resolved}. ` +\n      `Pass { allowProductionPath: true } for production CLI writes, or target a tmpdir-based path in tests.`,\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  async getHeadSha(): Promise<string | undefined> {\n    try {\n      const raw = await this.git.revparse(['--short', 'HEAD']);\n      const sha = raw.trim();\n      return sha.length > 0 ? sha : undefined;\n    } catch (err) {\n      log.error(`Failed to resolve HEAD: ${(err as Error).message}`);\n      return undefined;\n    }\n  }\n\n  async countCommitsBetween(base: string): Promise<number | undefined> {\n    try {\n      const raw = await this.git.raw(['rev-list', '--count', `${base}..HEAD`]);\n      const n = parseInt(raw.trim(), 10);\n      return Number.isFinite(n) && n >= 0 ? n : undefined;\n    } catch (err) {\n      log.error(`Failed to count commits since ${base}: ${(err as Error).message}`);\n      return undefined;\n    }\n  }\n}\n","import type { Database } from 'sql.js';\nimport type {\n  ISessionRecorderPort,\n  SessionEvent,\n  AggregatedStats,\n  ToolStats,\n  SymbolStats,\n  DetailLevelStats,\n} from '../../ports/i-session-recorder-port.js';\nimport { createLogger } from '../../core/logger.js';\n\nconst log = createLogger('ctxo:stats');\n\nexport class SessionRecorderAdapter implements ISessionRecorderPort {\n  private readonly db: Database;\n  private readonly onWrite: (() => void) | null;\n  private tableCreated = false;\n\n  constructor(db: Database, onWrite?: () => void) {\n    this.db = db;\n    this.onWrite = onWrite ?? null;\n  }\n\n  private ensureTable(): void {\n    if (this.tableCreated) return;\n    this.db.run(`\n      CREATE TABLE IF NOT EXISTS session_events (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        timestamp TEXT DEFAULT (datetime('now')),\n        tool TEXT NOT NULL,\n        symbol_id TEXT,\n        detail_level TEXT,\n        response_tokens INTEGER,\n        response_bytes INTEGER,\n        latency_ms REAL,\n        truncated BOOLEAN DEFAULT 0\n      )\n    `);\n    this.db.run('CREATE INDEX IF NOT EXISTS idx_session_timestamp ON session_events(timestamp)');\n    this.db.run('CREATE INDEX IF NOT EXISTS idx_session_tool ON session_events(tool)');\n    this.tableCreated = true;\n  }\n\n  record(event: SessionEvent): void {\n    try {\n      this.ensureTable();\n      this.db.run(\n        `INSERT INTO session_events (tool, symbol_id, detail_level, response_tokens, response_bytes, latency_ms, truncated)\n         VALUES (?, ?, ?, ?, ?, ?, ?)`,\n        [\n          event.tool,\n          event.symbolId,\n          event.detailLevel,\n          event.responseTokens,\n          event.responseBytes,\n          event.latencyMs,\n          event.truncated ? 1 : 0,\n        ],\n      );\n      this.flushToDisk();\n    } catch (err) {\n      log.error(`Failed to record session event: ${(err as Error).message}`);\n    }\n  }\n\n  queryStats(days?: number): AggregatedStats {\n    this.ensureTable();\n\n    const whereClause = days != null && days > 0\n      ? `WHERE timestamp >= datetime('now', '-${Math.floor(days)} days')`\n      : '';\n\n    // Total calls and tokens\n    const summaryResult = this.db.exec(\n      `SELECT COUNT(*) as total_calls, COALESCE(SUM(response_tokens), 0) as total_tokens\n       FROM session_events ${whereClause}`,\n    );\n    const summaryRow = summaryResult[0]?.values[0];\n    const totalCalls = Number(summaryRow?.[0] ?? 0);\n    const totalTokensServed = Number(summaryRow?.[1] ?? 0);\n\n    // Top tools\n    const toolsResult = this.db.exec(\n      `SELECT tool, COUNT(*) as calls, CAST(AVG(response_tokens) AS INTEGER) as avg_tokens\n       FROM session_events ${whereClause}\n       GROUP BY tool ORDER BY calls DESC LIMIT 5`,\n    );\n    const topTools: ToolStats[] = (toolsResult[0]?.values ?? []).map((row) => ({\n      tool: String(row[0]),\n      calls: Number(row[1]),\n      avgTokens: Number(row[2]),\n    }));\n\n    // Top symbols (exclude nulls)\n    const symbolWherePrefix = whereClause ? whereClause + ' AND' : 'WHERE';\n    const symbolsResult = this.db.exec(\n      `SELECT symbol_id, COUNT(*) as queries\n       FROM session_events ${symbolWherePrefix} symbol_id IS NOT NULL\n       GROUP BY symbol_id ORDER BY queries DESC LIMIT 5`,\n    );\n    const topSymbols: SymbolStats[] = (symbolsResult[0]?.values ?? []).map((row) => {\n      const symbolId = String(row[0]);\n      const parts = symbolId.split('::');\n      const name = parts.length >= 2 ? parts[1]! : symbolId;\n      return {\n        symbolId,\n        name,\n        queries: Number(row[1]),\n      };\n    });\n\n    // Detail level distribution\n    const levelResult = this.db.exec(\n      `SELECT detail_level, COUNT(*) as count\n       FROM session_events ${symbolWherePrefix} detail_level IS NOT NULL\n       GROUP BY detail_level ORDER BY detail_level`,\n    );\n    const levelRows = levelResult[0]?.values ?? [];\n    const levelTotal = levelRows.reduce((sum, row) => sum + Number(row[1]), 0);\n    const detailLevelDistribution: DetailLevelStats[] = levelRows.map((row) => ({\n      level: String(row[0]),\n      count: Number(row[1]),\n      percentage: levelTotal > 0 ? Math.round((Number(row[1]) / levelTotal) * 100) : 0,\n    }));\n\n    return {\n      totalCalls,\n      totalTokensServed,\n      topTools,\n      topSymbols,\n      detailLevelDistribution,\n    };\n  }\n\n  clear(): void {\n    this.ensureTable();\n    this.db.run('DELETE FROM session_events');\n    this.flushToDisk();\n  }\n\n  private flushToDisk(): void {\n    try {\n      this.onWrite?.();\n    } catch (err) {\n      log.error(`Failed to flush stats to disk: ${(err as Error).message}`);\n    }\n  }\n}\n","import { existsSync, readdirSync } from 'node:fs';\nimport { join, resolve } from 'node:path';\nimport type { IWorkspace, IPackage } from '@ctxo/plugin-api';\n\nconst MANIFEST_CANDIDATES = [\n  'package.json',\n  'pyproject.toml',\n  'setup.py',\n  'pom.xml',\n  'build.gradle',\n  'build.gradle.kts',\n  'go.mod',\n  'Cargo.toml',\n];\n\nfunction findManifest(dir: string): string {\n  for (const name of MANIFEST_CANDIDATES) {\n    const candidate = join(dir, name);\n    if (existsSync(candidate)) return candidate;\n  }\n  const csproj = findFirstByExt(dir, '.csproj') ?? findFirstByExt(dir, '.sln');\n  if (csproj) return csproj;\n  return join(dir, 'package.json');\n}\n\nfunction findFirstByExt(dir: string, ext: string): string | null {\n  try {\n    for (const entry of readdirSync(dir, { withFileTypes: true })) {\n      if (entry.isFile() && entry.name.endsWith(ext)) return join(dir, entry.name);\n    }\n  } catch {\n    // ignore\n  }\n  return null;\n}\n\n/**\n * v0.7 implementation: always returns a single-package workspace rooted at `cwd`.\n * Future Nx/Turborepo/pnpm workspace detectors implement the same interface.\n */\nexport function detectWorkspace(cwd: string): IWorkspace {\n  const root = resolve(cwd);\n  const pkg: IPackage = {\n    root,\n    manifest: findManifest(root),\n  };\n  return {\n    root,\n    packages: [pkg],\n  };\n}\n","import { existsSync, readFileSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { parse as parseYaml } from 'yaml';\nimport picomatch from 'picomatch';\nimport { createLogger } from '../logger.js';\nimport {\n  CtxoConfigSchema,\n  DEFAULT_CONFIG,\n  DEFAULT_WATCH_SNAPSHOT_MIN_FILE_CHANGES,\n  type CtxoConfig,\n} from './config-schema.js';\n\nconst log = createLogger('ctxo:config');\n\nexport interface LoadedConfig {\n  readonly config: CtxoConfig;\n  readonly errors: readonly string[];\n  readonly invalidGlobs: readonly string[];\n  readonly path: string;\n  readonly exists: boolean;\n}\n\nfunction isValidGlob(pattern: string): boolean {\n  try {\n    picomatch(pattern);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\nfunction validateGlobs(patterns: string[] | undefined, field: string, invalid: string[]): void {\n  if (!patterns) return;\n  for (const p of patterns) {\n    if (!isValidGlob(p)) invalid.push(`${field}: ${p}`);\n  }\n}\n\nexport function loadConfig(ctxoRoot: string): LoadedConfig {\n  const path = join(ctxoRoot, 'config.yaml');\n  const errors: string[] = [];\n  const invalidGlobs: string[] = [];\n\n  if (!existsSync(path)) {\n    return { config: DEFAULT_CONFIG, errors, invalidGlobs, path, exists: false };\n  }\n\n  let raw: string;\n  try {\n    raw = readFileSync(path, 'utf-8');\n  } catch (err) {\n    errors.push(`Cannot read ${path}: ${(err as Error).message}`);\n    return { config: DEFAULT_CONFIG, errors, invalidGlobs, path, exists: true };\n  }\n\n  let parsed: unknown;\n  try {\n    parsed = parseYaml(raw);\n  } catch (err) {\n    errors.push(`Invalid YAML in ${path}: ${(err as Error).message}`);\n    log.warn(`Invalid YAML in config.yaml, falling back to defaults: ${(err as Error).message}`);\n    return { config: DEFAULT_CONFIG, errors, invalidGlobs, path, exists: true };\n  }\n\n  if (parsed === null || parsed === undefined) {\n    return { config: DEFAULT_CONFIG, errors, invalidGlobs, path, exists: true };\n  }\n\n  const result = CtxoConfigSchema.safeParse(parsed);\n  if (!result.success) {\n    for (const issue of result.error.issues) {\n      errors.push(`${issue.path.join('.') || '<root>'}: ${issue.message}`);\n    }\n    log.warn(`Invalid config.yaml (${errors.length} issue(s)), falling back to defaults`);\n    return { config: DEFAULT_CONFIG, errors, invalidGlobs, path, exists: true };\n  }\n\n  validateGlobs(result.data.index?.ignore, 'index.ignore', invalidGlobs);\n  validateGlobs(result.data.index?.ignoreProjects, 'index.ignoreProjects', invalidGlobs);\n  for (const pattern of invalidGlobs) {\n    log.warn(`Invalid glob pattern in config.yaml — ${pattern}`);\n  }\n\n  return { config: result.data, errors, invalidGlobs, path, exists: true };\n}\n\nexport function statsEnabled(config: CtxoConfig): boolean {\n  return config.stats?.enabled !== false;\n}\n\nexport function indexIgnorePatterns(config: CtxoConfig): string[] {\n  return (config.index?.ignore ?? []).filter(isValidGlob);\n}\n\nexport function indexIgnoreProjectPatterns(config: CtxoConfig): string[] {\n  return (config.index?.ignoreProjects ?? []).filter(isValidGlob);\n}\n\nexport function maskingClusterLabelPatterns(config: CtxoConfig): string[] {\n  return (config.masking?.clusterLabels ?? []).filter(isValidGlob);\n}\n\nexport function watchSnapshotMinFileChanges(config: CtxoConfig): number {\n  const value = config.watch?.snapshotMinFileChanges;\n  if (typeof value === 'number' && Number.isFinite(value) && value >= 1) return value;\n  return DEFAULT_WATCH_SNAPSHOT_MIN_FILE_CHANGES;\n}\n\n/**\n * Build a single predicate that returns true when the given path matches any\n * of the supplied glob patterns. Paths are normalised to forward slashes.\n */\nexport function makeGlobMatcher(patterns: string[]): (path: string) => boolean {\n  if (patterns.length === 0) return () => false;\n  const matchers = patterns.map((p) => picomatch(p, { dot: true }));\n  return (input: string) => {\n    const normalised = input.replace(/\\\\/g, '/');\n    return matchers.some((m) => m(normalised));\n  };\n}\n","import { z } from 'zod';\n\n/**\n * Zod schema for `.ctxo/config.yaml`.\n *\n * Unknown fields on the root are ignored (forward compatibility) but unknown\n * fields under recognised sections (`stats`, `index`) are rejected so typos\n * surface immediately via `ctxo doctor`.\n */\nexport const StatsConfigSchema = z\n  .object({\n    enabled: z.boolean().optional(),\n  })\n  .strict();\n\nexport const IndexConfigSchema = z\n  .object({\n    ignore: z.array(z.string().min(1)).optional(),\n    ignoreProjects: z.array(z.string().min(1)).optional(),\n  })\n  .strict();\n\nexport const MaskingConfigSchema = z\n  .object({\n    /**\n     * Glob patterns matched against community cluster labels. Matching labels\n     * are replaced with `[masked-cluster-N]` in MCP tool responses so\n     * org-sensitive folder names (e.g. `src/payment-vault`, `internal-*`)\n     * never surface to AI agents over the stdio channel.\n     */\n    clusterLabels: z.array(z.string().min(1)).optional(),\n  })\n  .strict();\n\nexport const WatchConfigSchema = z\n  .object({\n    /**\n     * Minimum number of files that must be re-indexed since the last\n     * community snapshot before `ctxo watch` recomputes one. Default: 5.\n     * On large monorepos Louvain + PageRank cost ~1 s of blocking CPU;\n     * bumping this (e.g. 25) avoids recomputing on every save.\n     */\n    snapshotMinFileChanges: z.number().int().min(1).optional(),\n  })\n  .strict();\n\nexport const GateConfigSchema = z\n  .object({\n    enabled: z.boolean().optional(),\n    sensitivity: z.enum(['strict', 'balanced', 'lenient']).optional(),\n    /** Absolute floor: minimum confirmed+likely dependents before the gate can fire. */\n    minDependents: z.number().int().min(0).optional(),\n    /** Repo-relative significance: symbol must be in the top `percentile`% by PageRank. */\n    percentile: z.number().int().min(1).max(100).optional(),\n  })\n  .strict();\n\nexport const CtxoConfigSchema = z\n  .object({\n    version: z.union([z.string(), z.number()]).optional(),\n    stats: StatsConfigSchema.optional(),\n    index: IndexConfigSchema.optional(),\n    masking: MaskingConfigSchema.optional(),\n    watch: WatchConfigSchema.optional(),\n    gate: GateConfigSchema.optional(),\n  })\n  .passthrough();\n\nexport type StatsConfig = z.infer<typeof StatsConfigSchema>;\nexport type IndexConfig = z.infer<typeof IndexConfigSchema>;\nexport type MaskingConfig = z.infer<typeof MaskingConfigSchema>;\nexport type WatchConfig = z.infer<typeof WatchConfigSchema>;\nexport type GateConfig = z.infer<typeof GateConfigSchema>;\nexport type CtxoConfig = z.infer<typeof CtxoConfigSchema>;\n\nexport const DEFAULT_WATCH_SNAPSHOT_MIN_FILE_CHANGES = 5;\n\nexport const DEFAULT_CONFIG: CtxoConfig = {\n  version: '1.0',\n  stats: { enabled: true },\n  index: { ignore: [], ignoreProjects: [] },\n  masking: { clusterLabels: [] },\n  watch: { snapshotMinFileChanges: DEFAULT_WATCH_SNAPSHOT_MIN_FILE_CHANGES },\n  gate: { enabled: true, sensitivity: 'balanced' },\n};\n","import type { SymbolNode, GraphEdge } from '../types.js';\n\nexport class SymbolGraph {\n  private readonly nodes = new Map<string, SymbolNode>();\n  private readonly nodesByFileAndName = new Map<string, SymbolNode>();\n  private readonly forwardEdges = new Map<string, GraphEdge[]>();\n  private readonly reverseEdges = new Map<string, GraphEdge[]>();\n  private edgeSet = new Set<string>();\n\n  addNode(node: SymbolNode): void {\n    this.nodes.set(node.symbolId, node);\n    // Index by file::name (ignoring kind) for fuzzy edge resolution\n    const [p0, p1] = node.symbolId.split('::');\n    if (p0 !== undefined && p1 !== undefined) {\n      this.nodesByFileAndName.set(`${p0}::${p1}`, node);\n    }\n  }\n\n  addEdge(edge: GraphEdge): void {\n    // Resolve edge endpoints: if exact ID not found, try fuzzy match by file::name\n    const resolvedFrom = this.resolveNodeId(edge.from);\n    const resolvedTo = this.resolveNodeId(edge.to);\n    const resolvedEdge: GraphEdge = { from: resolvedFrom, to: resolvedTo, kind: edge.kind };\n\n    const edgeKey = `${resolvedEdge.from}|${resolvedEdge.to}|${resolvedEdge.kind}`;\n    if (this.edgeSet.has(edgeKey)) return;\n    this.edgeSet.add(edgeKey);\n\n    const forward = this.forwardEdges.get(resolvedEdge.from) ?? [];\n    forward.push(resolvedEdge);\n    this.forwardEdges.set(resolvedEdge.from, forward);\n\n    const reverse = this.reverseEdges.get(resolvedEdge.to) ?? [];\n    reverse.push(resolvedEdge);\n    this.reverseEdges.set(resolvedEdge.to, reverse);\n  }\n\n  getNode(symbolId: string): SymbolNode | undefined {\n    return this.nodes.get(symbolId) ?? this.resolveNodeFuzzy(symbolId);\n  }\n\n  private resolveNodeId(id: string): string {\n    if (this.nodes.has(id)) return id;\n    const [p0, p1] = id.split('::');\n    if (p0 !== undefined && p1 !== undefined) {\n      const fuzzyKey = `${p0}::${p1}`;\n      const match = this.nodesByFileAndName.get(fuzzyKey);\n      if (match) return match.symbolId;\n\n      // Try .js → .ts extension swap (handles unresolved module specifiers)\n      const jsToTs = p0.replace(/\\.js$/, '.ts');\n      if (jsToTs !== p0) {\n        const altKey = `${jsToTs}::${p1}`;\n        const altMatch = this.nodesByFileAndName.get(altKey);\n        if (altMatch) return altMatch.symbolId;\n      }\n    }\n    return id;\n  }\n\n  private resolveNodeFuzzy(id: string): SymbolNode | undefined {\n    const [p0, p1] = id.split('::');\n    if (p0 !== undefined && p1 !== undefined) {\n      const match = this.nodesByFileAndName.get(`${p0}::${p1}`);\n      if (match) return match;\n\n      // Try .js → .ts extension swap (consistent with resolveNodeId)\n      const jsToTs = p0.replace(/\\.js$/, '.ts');\n      if (jsToTs !== p0) {\n        return this.nodesByFileAndName.get(`${jsToTs}::${p1}`);\n      }\n    }\n    return undefined;\n  }\n\n  getForwardEdges(symbolId: string): GraphEdge[] {\n    return this.forwardEdges.get(symbolId) ?? [];\n  }\n\n  getReverseEdges(symbolId: string): GraphEdge[] {\n    return this.reverseEdges.get(symbolId) ?? [];\n  }\n\n  hasNode(symbolId: string): boolean {\n    return this.nodes.has(symbolId) || this.resolveNodeFuzzy(symbolId) !== undefined;\n  }\n\n  get nodeCount(): number {\n    return this.nodes.size;\n  }\n\n  get edgeCount(): number {\n    return this.edgeSet.size;\n  }\n\n  allNodes(): SymbolNode[] {\n    return [...this.nodes.values()];\n  }\n\n  allEdges(): GraphEdge[] {\n    const edges: GraphEdge[] = [];\n    for (const list of this.forwardEdges.values()) {\n      edges.push(...list);\n    }\n    return edges;\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 { CommunityEntry, CommunitySnapshot, DriftEvent } from '../types.js';\n\nexport type DriftStability = 'stable' | 'transient' | 'unverified';\n\nexport interface DriftEventWithStability extends DriftEvent {\n  readonly stability: DriftStability;\n}\n\nexport interface DriftStabilitySummary {\n  /** Events confirmed across ≥2 snapshots (real drift). */\n  readonly stable: number;\n  /** Events that bounced back to a prior cluster (likely Louvain jitter). */\n  readonly transient: number;\n  /** Events seen only once because history is too shallow to classify. */\n  readonly unverified: number;\n}\n\nexport interface DriftDetectionResult {\n  readonly events: DriftEventWithStability[];\n  readonly confidence: 'high' | 'medium' | 'low';\n  readonly snapshotsAvailable: number;\n  readonly stability: DriftStabilitySummary;\n  readonly hint?: string;\n}\n\n// Issue #56: lowered from 0.5 → 0.3 to be more forgiving when Louvain\n// renumbers clusters between runs. Jaccard 0.3 still requires meaningful\n// membership overlap but tolerates routine re-clustering.\nconst DEFAULT_JACCARD_THRESHOLD = 0.3;\n\nexport interface DriftDetectorOptions {\n  readonly jaccardThreshold?: number;\n  /**\n   * Filter out transient drift — i.e., events where the symbol bounced back\n   * to a previously-seen cluster within the retained snapshot window. Enabled\n   * by default so callers don't have to wade through Louvain jitter.\n   */\n  readonly suppressTransient?: boolean;\n}\n\nexport class DriftDetector {\n  private readonly jaccardThreshold: number;\n  private readonly suppressTransient: boolean;\n\n  constructor(options: DriftDetectorOptions = {}) {\n    this.jaccardThreshold = options.jaccardThreshold ?? DEFAULT_JACCARD_THRESHOLD;\n    this.suppressTransient = options.suppressTransient ?? true;\n  }\n\n  detect(\n    current: CommunitySnapshot,\n    history: readonly CommunitySnapshot[],\n  ): DriftDetectionResult {\n    const snapshotsAvailable = history.length;\n    const previous = history[0];\n    const anchor = history[1];\n\n    if (!previous) {\n      return {\n        events: [],\n        confidence: 'low',\n        snapshotsAvailable,\n        stability: { stable: 0, transient: 0, unverified: 0 },\n        hint: 'No prior snapshot available — install the post-commit hook (`ctxo init`), run `ctxo watch`, or add `ctxo index --check` to CI so the drift history accumulates.',\n      };\n    }\n\n    const currentByCommunityId = indexByCommunityId(current.communities);\n    const previousByCommunityId = indexByCommunityId(previous.communities);\n    const mapping = this.mapCommunities(currentByCommunityId, previousByCommunityId);\n\n    const currentAssignments = assignmentMap(current.communities);\n    const previousAssignments = assignmentMap(previous.communities);\n    const anchorAssignments = anchor ? assignmentMap(anchor.communities) : undefined;\n    const previousLabels = labelMap(previous.communities);\n    const currentLabels = labelMap(current.communities);\n\n    // Compute anchor→previous mapping so we can translate the symbol's anchor\n    // cluster id into the \"previous snapshot\" id space for comparison.\n    const anchorToPrev = anchor\n      ? this.mapCommunities(previousByCommunityId, indexByCommunityId(anchor.communities))\n      : new Map<number, number>();\n\n    const rawEvents: DriftEventWithStability[] = [];\n    const stability = { stable: 0, transient: 0, unverified: 0 };\n\n    for (const [symbolId, currentId] of currentAssignments) {\n      const prevId = previousAssignments.get(symbolId);\n      if (prevId === undefined) continue;\n      const mappedPrevId = mapping.get(prevId);\n      if (mappedPrevId === currentId) continue;\n\n      // Stability classification:\n      //   stable    — anchor's cluster maps to `prevId` (the symbol was settled in the\n      //               prior cluster for ≥2 snapshots, then moved; real drift).\n      //   transient — anchor's cluster maps to `currentId` (the symbol bounced between\n      //               clusters; likely Louvain jitter — worth suppressing by default).\n      //   unverified — no anchor snapshot, or anchor has no entry for this symbol.\n      let classification: DriftStability;\n      if (!anchorAssignments) {\n        classification = 'unverified';\n      } else {\n        const anchorId = anchorAssignments.get(symbolId);\n        if (anchorId === undefined) {\n          classification = 'unverified';\n        } else {\n          const anchorInPrevSpace = anchorToPrev.get(anchorId);\n          if (anchorInPrevSpace === prevId) {\n            classification = 'stable';\n          } else if (anchorInPrevSpace !== undefined) {\n            // Anchor maps to some previous cluster that is not the movedFrom cluster.\n            // If that translates forward to the current cluster, this is a bounce.\n            const anchorInCurrentSpace = mapping.get(anchorInPrevSpace);\n            classification =\n              anchorInCurrentSpace === currentId ? 'transient' : 'unverified';\n          } else {\n            classification = 'unverified';\n          }\n        }\n      }\n\n      stability[classification]++;\n      rawEvents.push({\n        symbolId,\n        movedFrom: {\n          id: prevId,\n          label: previousLabels.get(prevId) ?? `community-${prevId}`,\n        },\n        movedTo: {\n          id: currentId,\n          label: currentLabels.get(currentId) ?? `community-${currentId}`,\n        },\n        firstSeenInNewCluster: current.computedAt,\n        stability: classification,\n      });\n    }\n\n    const events = (this.suppressTransient\n      ? rawEvents.filter((e) => e.stability !== 'transient')\n      : rawEvents\n    ).sort((a, b) => a.symbolId.localeCompare(b.symbolId));\n\n    return {\n      events,\n      confidence: confidenceFor(snapshotsAvailable),\n      snapshotsAvailable,\n      stability,\n      hint: hintFor(snapshotsAvailable),\n    };\n  }\n\n  private mapCommunities(\n    current: ReadonlyMap<number, Set<string>>,\n    previous: ReadonlyMap<number, Set<string>>,\n  ): Map<number, number> {\n    // For each previous-community, pick the current-community with highest Jaccard.\n    const mapping = new Map<number, number>();\n    for (const [prevId, prevMembers] of previous) {\n      let bestCurrentId: number | undefined;\n      let bestOverlap = 0;\n      for (const [currentId, currentMembers] of current) {\n        const overlap = jaccard(prevMembers, currentMembers);\n        if (overlap > bestOverlap) {\n          bestOverlap = overlap;\n          bestCurrentId = currentId;\n        }\n      }\n      if (bestCurrentId !== undefined && bestOverlap >= this.jaccardThreshold) {\n        mapping.set(prevId, bestCurrentId);\n      }\n    }\n    return mapping;\n  }\n}\n\nfunction indexByCommunityId(\n  entries: readonly CommunityEntry[],\n): Map<number, Set<string>> {\n  const index = new Map<number, Set<string>>();\n  for (const entry of entries) {\n    const bucket = index.get(entry.communityId) ?? new Set<string>();\n    bucket.add(entry.symbolId);\n    index.set(entry.communityId, bucket);\n  }\n  return index;\n}\n\nfunction assignmentMap(entries: readonly CommunityEntry[]): Map<string, number> {\n  const map = new Map<string, number>();\n  for (const entry of entries) {\n    map.set(entry.symbolId, entry.communityId);\n  }\n  return map;\n}\n\nfunction labelMap(entries: readonly CommunityEntry[]): Map<number, string> {\n  const labels = new Map<number, string>();\n  for (const entry of entries) {\n    if (!labels.has(entry.communityId)) {\n      labels.set(entry.communityId, entry.communityLabel);\n    }\n  }\n  return labels;\n}\n\nfunction jaccard(a: ReadonlySet<string>, b: ReadonlySet<string>): number {\n  if (a.size === 0 && b.size === 0) return 1;\n  let intersection = 0;\n  for (const x of a) if (b.has(x)) intersection++;\n  const union = a.size + b.size - intersection;\n  return union === 0 ? 0 : intersection / union;\n}\n\nfunction confidenceFor(snapshots: number): 'high' | 'medium' | 'low' {\n  if (snapshots >= 7) return 'high';\n  if (snapshots >= 3) return 'medium';\n  return 'low';\n}\n\nfunction hintFor(snapshots: number): string | undefined {\n  if (snapshots >= 3) return undefined;\n  return 'Install post-commit hook or run `ctxo index` more often to build a richer drift history.';\n}\n","import type { SymbolGraph } from '../graph/symbol-graph.js';\nimport type { CoChangeEntry } from '../types.js';\n\nexport type ImpactConfidence = 'confirmed' | 'likely' | 'potential';\n\nexport interface BlastRadiusEntry {\n  readonly symbolId: string;\n  readonly depth: number;\n  readonly dependentCount: number;\n  readonly riskScore: number;\n  readonly confidence: ImpactConfidence;\n  readonly edgeKinds: string[];\n  readonly coChangeFrequency?: number;\n}\n\nexport interface BlastRadiusResult {\n  readonly impactedSymbols: BlastRadiusEntry[];\n  readonly directDependentsCount: number;\n  readonly confirmedCount: number;\n  readonly likelyCount: number;\n  readonly potentialCount: number;\n  readonly overallRiskScore: number;\n}\n\nconst CONFIRMED_KINDS = new Set(['calls', 'extends', 'implements']);\nconst LIKELY_KINDS = new Set(['uses']);\n\nconst CONFIDENCE_RANK: Record<ImpactConfidence, number> = {\n  confirmed: 2,\n  likely: 1,\n  potential: 0,\n};\n\nfunction edgeKindToConfidence(kind: string): ImpactConfidence {\n  if (CONFIRMED_KINDS.has(kind)) return 'confirmed';\n  if (LIKELY_KINDS.has(kind)) return 'likely';\n  return 'potential';\n}\n\nexport class BlastRadiusCalculator {\n  calculate(graph: SymbolGraph, symbolId: string, coChangeMap?: Map<string, CoChangeEntry[]>): BlastRadiusResult {\n    if (!graph.hasNode(symbolId)) {\n      return { impactedSymbols: [], directDependentsCount: 0, confirmedCount: 0, likelyCount: 0, potentialCount: 0, overallRiskScore: 0 };\n    }\n\n    const sourceFile = symbolId.split('::')[0]!;\n\n    const visited = new Set<string>([symbolId]);\n    const rawEntries: Array<{ symbolId: string; depth: number; riskScore: number; confidence: ImpactConfidence; edgeKinds: string[]; coChangeFrequency?: number }> = [];\n\n    // BFS via reverse edges (who depends on this symbol?)\n    const queue: Array<{ id: string; depth: number }> = [{ id: symbolId, depth: 0 }];\n\n    while (queue.length > 0) {\n      const current = queue.shift()!;\n\n      const reverseEdges = graph.getReverseEdges(current.id);\n\n      // Group edges by source node, pick strongest confidence per node\n      // confirmed > likely > potential — collect all edge kinds\n      const bestByNode = new Map<string, { confidence: ImpactConfidence; kinds: Set<string> }>();\n      for (const edge of reverseEdges) {\n        if (visited.has(edge.from)) continue;\n        const conf = edgeKindToConfidence(edge.kind);\n        const existing = bestByNode.get(edge.from);\n        if (!existing) {\n          bestByNode.set(edge.from, { confidence: conf, kinds: new Set([edge.kind]) });\n        } else {\n          existing.kinds.add(edge.kind);\n          if (CONFIDENCE_RANK[conf] > CONFIDENCE_RANK[existing.confidence]) {\n            existing.confidence = conf;\n          }\n        }\n      }\n\n      for (const [nodeId, info] of bestByNode) {\n        visited.add(nodeId);\n        // Keep orphan edge sources (common for test/config files that only\n        // import — ts-morph writes their synthetic \"file-module\" symbolId to\n        // the edge's `from` but never to the file's symbols[] array). BFS\n        // into an orphan terminates naturally since getReverseEdges returns [].\n\n        const depth = current.depth + 1;\n        const riskScore = 1 / Math.pow(depth, 0.7);\n\n        // Co-change boost: if files frequently change together, upgrade potential → likely\n        let confidence = info.confidence;\n        let coChangeFrequency: number | undefined;\n        if (coChangeMap) {\n          const nodeFile = nodeId.split('::')[0]!;\n          const coEntries = coChangeMap.get(sourceFile);\n          if (coEntries) {\n            const match = coEntries.find(e => e.file1 === nodeFile || e.file2 === nodeFile);\n            if (match) {\n              coChangeFrequency = match.frequency;\n              if (confidence === 'potential' && match.frequency > 0.5) {\n                confidence = 'likely';\n              }\n            }\n          }\n        }\n\n        rawEntries.push({\n          symbolId: nodeId,\n          depth,\n          riskScore: Math.round(riskScore * 1000) / 1000,\n          confidence,\n          edgeKinds: [...info.kinds],\n          coChangeFrequency,\n        });\n\n        queue.push({ id: nodeId, depth });\n      }\n    }\n\n    // GAP-30 FIX: compute dependentCount as blast-scope in-degree (not global)\n    const blastSet = new Set(rawEntries.map((e) => e.symbolId));\n    blastSet.add(symbolId);\n\n    const entries: BlastRadiusEntry[] = rawEntries.map((e) => ({\n      ...e,\n      dependentCount: graph.getReverseEdges(e.symbolId).filter((re) => blastSet.has(re.from)).length,\n    }));\n\n    // Sort by depth ascending\n    entries.sort((a, b) => a.depth - b.depth);\n\n    const directDependentsCount = entries.filter((e) => e.depth === 1).length;\n\n    // GAP-29 FIX: depth-weighted risk — direct dependents dominate\n    const totalRisk = entries.reduce((sum, e) => sum + e.riskScore, 0);\n    const overallRiskScore = Math.round(Math.min(totalRisk / Math.max(directDependentsCount, 1), 1) * 1000) / 1000;\n\n    const confirmedCount = entries.filter((e) => e.confidence === 'confirmed').length;\n    const likelyCount = entries.filter((e) => e.confidence === 'likely').length;\n    const potentialCount = entries.filter((e) => e.confidence === 'potential').length;\n\n    return { impactedSymbols: entries, directDependentsCount, confirmedCount, likelyCount, potentialCount, overallRiskScore };\n  }\n}\n","export interface LayerRule {\n  readonly pattern: RegExp;\n  readonly layer: string;\n}\n\nexport interface OverlayResult {\n  readonly layers: Record<string, string[]>;\n}\n\nconst DEFAULT_RULES: LayerRule[] = [\n  // Test layer (matched first — __tests__, .test.ts, tests/, fixtures)\n  { pattern: /__tests__/, layer: 'Test' },\n  { pattern: /\\.test\\.ts$/, layer: 'Test' },\n  { pattern: /\\btests\\b/, layer: 'Test' },\n  { pattern: /\\bfixtures?\\b/, layer: 'Test' },\n  // Composition root\n  { pattern: /src\\/index\\.ts$/, layer: 'Composition' },\n  // Domain\n  { pattern: /\\bcore\\b/, layer: 'Domain' },\n  { pattern: /\\bports?\\b/, layer: 'Domain' },\n  // Adapter\n  { pattern: /\\badapters?\\b/, layer: 'Adapter' },\n  { pattern: /\\bcli\\b/, layer: 'Adapter' },\n  // Infrastructure\n  { pattern: /\\binfra\\b/, layer: 'Infrastructure' },\n  { pattern: /\\bdb\\b/, layer: 'Infrastructure' },\n  { pattern: /\\bqueue\\b/, layer: 'Infrastructure' },\n  // Config files\n  { pattern: /\\.(config|rc)\\.(ts|js|json)$/, layer: 'Configuration' },\n];\n\nexport class ArchitecturalOverlay {\n  private readonly rules: LayerRule[];\n\n  constructor(customRules?: LayerRule[]) {\n    this.rules = (customRules ?? DEFAULT_RULES).map(({ pattern, layer }) => ({\n      pattern: new RegExp(pattern.source, pattern.flags),\n      layer,\n    }));\n  }\n\n  classify(filePaths: readonly string[]): OverlayResult {\n    const layers: Record<string, string[]> = {};\n\n    for (const filePath of filePaths) {\n      const layer = this.matchLayer(filePath);\n      const list = layers[layer] ?? [];\n      list.push(filePath);\n      layers[layer] = list;\n    }\n\n    return { layers };\n  }\n\n  private matchLayer(filePath: string): string {\n    for (const rule of this.rules) {\n      if (rule.pattern.test(filePath)) {\n        return rule.layer;\n      }\n    }\n    return 'Unknown';\n  }\n}\n","import type { SymbolGraph } from '../graph/symbol-graph.js';\nimport type { SymbolKind } from '../types.js';\n\nexport type DeadCodeConfidence = 1.0 | 0.9 | 0.7;\n\nexport interface DeadSymbolEntry {\n  readonly symbolId: string;\n  readonly file: string;\n  readonly name: string;\n  readonly kind: SymbolKind;\n  readonly confidence: DeadCodeConfidence;\n  readonly reason: string;\n  readonly cascadeDepth?: number;\n}\n\nexport interface UnusedExportEntry {\n  readonly symbolId: string;\n  readonly file: string;\n  readonly name: string;\n  readonly kind: SymbolKind;\n}\n\nexport interface ScaffoldingEntry {\n  readonly file: string;\n  readonly line: number;\n  readonly pattern: string;\n  readonly text: string;\n}\n\nexport interface DeadCodeResult {\n  readonly totalSymbols: number;\n  readonly reachableSymbols: number;\n  readonly deadSymbols: DeadSymbolEntry[];\n  readonly unusedExports: UnusedExportEntry[];\n  readonly deadFiles: string[];\n  readonly scaffolding: ScaffoldingEntry[];\n  readonly deadCodePercentage: number;\n}\n\n// Patterns for files to exclude from dead code analysis\nconst TEST_PATTERNS = [/__tests__/, /\\.test\\.ts$/, /\\.spec\\.ts$/, /\\btests\\//, /\\bfixtures?\\//];\nconst CONFIG_PATTERNS = [/\\.(config|rc)\\.(ts|js|json)$/, /tsconfig/, /eslint/, /\\.d\\.ts$/];\n\n// Framework lifecycle symbols — should never be flagged as dead\nconst FRAMEWORK_PATTERNS = [\n  // Vitest\n  /^(describe|it|expect|beforeAll|beforeEach|afterAll|afterEach|vi)$/,\n  // MCP SDK\n  /^(registerTool|registerPrompt|connect|close)$/,\n  // Zod schemas (conventionally exported for validation)\n  /Schema$/,\n  // Node.js lifecycle\n  /^main$/,\n];\n\n// Scaffolding / AI artifact patterns\nconst SCAFFOLDING_PATTERNS = [\n  { regex: /\\bTODO\\b/i, pattern: 'TODO' },\n  { regex: /\\bFIXME\\b/i, pattern: 'FIXME' },\n  { regex: /\\bHACK\\b/i, pattern: 'HACK' },\n  { regex: /\\bPLACEHOLDER\\b/i, pattern: 'PLACEHOLDER' },\n  { regex: /\\bXXX\\b/, pattern: 'XXX' },\n  { regex: /Phase\\s+\\d|Step\\s+\\d/i, pattern: 'PHASE/STEP' },\n  { regex: /not\\s+(?:yet\\s+)?implement/i, pattern: 'NOT_IMPLEMENTED' },\n  { regex: /temporary|temp\\s+fix/i, pattern: 'TEMPORARY' },\n];\n\nexport class DeadCodeDetector {\n  detect(\n    graph: SymbolGraph,\n    options: { includeTests?: boolean; sourceContents?: Map<string, string> } = {},\n  ): DeadCodeResult {\n    const allNodes = graph.allNodes();\n\n    // Filter candidates — exclude tests/config by default\n    const candidates = options.includeTests\n      ? allNodes\n      : allNodes.filter((n) => {\n          const file = n.symbolId.split('::')[0] ?? '';\n          return !this.matchesAny(file, TEST_PATTERNS) && !this.matchesAny(file, CONFIG_PATTERNS);\n        });\n\n    if (candidates.length === 0) {\n      return { totalSymbols: 0, reachableSymbols: 0, deadSymbols: [], unusedExports: [], deadFiles: [], scaffolding: this.detectScaffolding(options.sourceContents), deadCodePercentage: 0 };\n    }\n\n    // Dynamic entry point detection: symbols with zero reverse edges (no one imports them)\n    const candidateIds = new Set(candidates.map((n) => n.symbolId));\n    const entryPoints = new Set<string>();\n\n    for (const node of candidates) {\n      // Framework lifecycle symbols are always entry points (never dead)\n      if (this.isFrameworkSymbol(node.name)) {\n        entryPoints.add(node.symbolId);\n        continue;\n      }\n\n      const reverseEdges = graph.getReverseEdges(node.symbolId);\n      const forwardEdges = graph.getForwardEdges(node.symbolId);\n\n      // Filter: only count reverse edges from OTHER candidates\n      const incomingFromCandidates = reverseEdges.filter((e) => candidateIds.has(e.from) && e.from !== node.symbolId);\n\n      if (incomingFromCandidates.length === 0) {\n        const hasOutgoing = forwardEdges.some((e) => candidateIds.has(e.to));\n        if (hasOutgoing || reverseEdges.length > 0) {\n          entryPoints.add(node.symbolId);\n        }\n      }\n    }\n\n    // Forward BFS from all entry points — mark reachable symbols\n    const reachable = new Set<string>();\n    const queue = [...entryPoints];\n\n    while (queue.length > 0) {\n      const current = queue.shift()!;\n      if (reachable.has(current)) continue;\n      reachable.add(current);\n\n      for (const edge of graph.getForwardEdges(current)) {\n        if (!reachable.has(edge.to) && candidateIds.has(edge.to)) {\n          queue.push(edge.to);\n        }\n      }\n    }\n\n    // Dead = candidates not reachable from any entry point\n    // These are \"island\" symbols — circular deps where the whole cluster is unreachable\n    const deadIds = new Set<string>();\n    for (const node of candidates) {\n      if (!reachable.has(node.symbolId)) {\n        deadIds.add(node.symbolId);\n      }\n    }\n\n    // Compute cascade depth: how deep in the dead chain is this symbol?\n    const cascadeDepthMap = this.computeCascadeDepths(graph, deadIds, candidateIds);\n\n    // Compute confidence per dead symbol\n    const deadSymbols: DeadSymbolEntry[] = [];\n    for (const node of candidates) {\n      if (!deadIds.has(node.symbolId)) continue;\n\n      const file = node.symbolId.split('::')[0] ?? '';\n      const confidence = this.computeConfidence(graph, node.symbolId, deadIds);\n      const cascadeDepth = cascadeDepthMap.get(node.symbolId);\n\n      deadSymbols.push({\n        symbolId: node.symbolId,\n        file,\n        name: node.name,\n        kind: node.kind,\n        confidence,\n        reason: this.describeReason(confidence),\n        ...(cascadeDepth !== undefined && cascadeDepth > 0 ? { cascadeDepth } : {}),\n      });\n    }\n\n    // Dead files = files where ALL candidate symbols are dead\n    const fileStats = new Map<string, { total: number; dead: number }>();\n    for (const node of candidates) {\n      const file = node.symbolId.split('::')[0] ?? '';\n      const stats = fileStats.get(file) ?? { total: 0, dead: 0 };\n      stats.total++;\n      if (deadIds.has(node.symbolId)) stats.dead++;\n      fileStats.set(file, stats);\n    }\n\n    const deadFiles = [...fileStats.entries()]\n      .filter(([, s]) => s.total > 0 && s.dead === s.total)\n      .map(([file]) => file);\n\n    // Unused exports: symbols with zero reverse edges from other candidates\n    // Different from dead code: an unused export may be an entry point (reachable)\n    // but still never imported by anyone\n    const unusedExports: UnusedExportEntry[] = [];\n    for (const node of candidates) {\n      const reverseEdges = graph.getReverseEdges(node.symbolId);\n      const externalImporters = reverseEdges.filter((e) =>\n        candidateIds.has(e.from) && e.from !== node.symbolId,\n      );\n\n      if (externalImporters.length === 0 && !deadIds.has(node.symbolId)) {\n        // Exported, reachable (entry point), but nobody imports it\n        unusedExports.push({\n          symbolId: node.symbolId,\n          file: node.symbolId.split('::')[0] ?? '',\n          name: node.name,\n          kind: node.kind,\n        });\n      }\n    }\n\n    // Scaffolding detection: scan source contents for TODO/FIXME/HACK patterns\n    const scaffolding = this.detectScaffolding(options.sourceContents);\n\n    const deadCodePercentage = Math.round((deadSymbols.length / candidates.length) * 100 * 10) / 10;\n\n    return {\n      totalSymbols: candidates.length,\n      reachableSymbols: reachable.size,\n      deadSymbols,\n      unusedExports,\n      deadFiles,\n      scaffolding,\n      deadCodePercentage,\n    };\n  }\n\n  private computeConfidence(\n    graph: SymbolGraph,\n    symbolId: string,\n    deadIds: Set<string>,\n  ): DeadCodeConfidence {\n    const reverseEdges = graph.getReverseEdges(symbolId);\n\n    // 1.0: Zero importers at all — definitely dead\n    if (reverseEdges.length === 0) {\n      return 1.0;\n    }\n\n    // 0.9: Has importers but they're all from test/config files\n    const allImportersExcluded = reverseEdges.every((e) => {\n      const importerFile = e.from.split('::')[0] ?? '';\n      return this.matchesAny(importerFile, TEST_PATTERNS) || this.matchesAny(importerFile, CONFIG_PATTERNS);\n    });\n    if (allImportersExcluded) {\n      return 0.9;\n    }\n\n    // 0.7: All importers are themselves dead (cascading dead code)\n    const allImportersDead = reverseEdges.every((e) => deadIds.has(e.from));\n    if (allImportersDead) {\n      return 0.7;\n    }\n\n    // Shouldn't reach here if symbol is truly dead, but default to 0.7\n    return 0.7;\n  }\n\n  private describeReason(confidence: DeadCodeConfidence): string {\n    switch (confidence) {\n      case 1.0:\n        return 'Zero importers — no code references this symbol';\n      case 0.9:\n        return 'Only referenced from test/config files';\n      case 0.7:\n        return 'All importers are themselves dead (cascading)';\n    }\n  }\n\n  private isFrameworkSymbol(name: string): boolean {\n    return FRAMEWORK_PATTERNS.some((p) => p.test(name));\n  }\n\n  private computeCascadeDepths(\n    graph: SymbolGraph,\n    deadIds: Set<string>,\n    candidateIds: Set<string>,\n  ): Map<string, number> {\n    const depths = new Map<string, number>();\n\n    // Find root dead symbols (zero reverse edges from other dead symbols)\n    const rootDead = new Set<string>();\n    for (const id of deadIds) {\n      const reverseEdges = graph.getReverseEdges(id);\n      const deadImporters = reverseEdges.filter((e) => deadIds.has(e.from) && e.from !== id);\n      if (deadImporters.length === 0) {\n        rootDead.add(id);\n        depths.set(id, 0);\n      }\n    }\n\n    // BFS from root dead symbols to compute cascade depth\n    const queue = [...rootDead].map((id) => ({ id, depth: 0 }));\n    const visited = new Set(rootDead);\n\n    while (queue.length > 0) {\n      const current = queue.shift()!;\n      for (const edge of graph.getForwardEdges(current.id)) {\n        if (deadIds.has(edge.to) && !visited.has(edge.to) && candidateIds.has(edge.to)) {\n          const newDepth = current.depth + 1;\n          depths.set(edge.to, newDepth);\n          visited.add(edge.to);\n          queue.push({ id: edge.to, depth: newDepth });\n        }\n      }\n    }\n\n    return depths;\n  }\n\n  private detectScaffolding(sourceContents?: Map<string, string>): ScaffoldingEntry[] {\n    if (!sourceContents || sourceContents.size === 0) return [];\n\n    const results: ScaffoldingEntry[] = [];\n\n    for (const [file, content] of sourceContents) {\n      // Skip test/config files\n      if (this.matchesAny(file, TEST_PATTERNS) || this.matchesAny(file, CONFIG_PATTERNS)) continue;\n\n      const lines = content.split('\\n');\n      for (let i = 0; i < lines.length; i++) {\n        const line = lines[i]!;\n        for (const { regex, pattern } of SCAFFOLDING_PATTERNS) {\n          if (regex.test(line)) {\n            results.push({\n              file,\n              line: i + 1,\n              pattern,\n              text: line.trim().slice(0, 120),\n            });\n            break; // One match per line\n          }\n        }\n      }\n    }\n\n    return results;\n  }\n\n  private matchesAny(value: string, patterns: RegExp[]): boolean {\n    return patterns.some((p) => p.test(value));\n  }\n}\n","import type { SymbolGraph } from '../graph/symbol-graph.js';\n\nexport interface PageRankEntry {\n  readonly symbolId: string;\n  readonly name: string;\n  readonly kind: string;\n  readonly file: string;\n  readonly score: number;\n  readonly inDegree: number;\n  readonly outDegree: number;\n}\n\nexport interface PageRankResult {\n  readonly rankings: PageRankEntry[];\n  readonly totalSymbols: number;\n  readonly iterations: number;\n  readonly converged: boolean;\n}\n\nexport interface PageRankOptions {\n  readonly damping?: number;\n  readonly maxIterations?: number;\n  readonly tolerance?: number;\n  readonly limit?: number;\n}\n\nconst DEFAULT_DAMPING = 0.85;\nconst DEFAULT_MAX_ITERATIONS = 100;\nconst DEFAULT_TOLERANCE = 1e-6;\nconst DEFAULT_LIMIT = 25;\n\nexport class PageRankCalculator {\n  calculate(graph: SymbolGraph, options: PageRankOptions = {}): PageRankResult {\n    const damping = options.damping ?? DEFAULT_DAMPING;\n    const maxIterations = options.maxIterations ?? DEFAULT_MAX_ITERATIONS;\n    const tolerance = options.tolerance ?? DEFAULT_TOLERANCE;\n    const limit = options.limit ?? DEFAULT_LIMIT;\n\n    const nodes = graph.allNodes();\n    const n = nodes.length;\n\n    if (n === 0) {\n      return { rankings: [], totalSymbols: 0, iterations: 0, converged: true };\n    }\n\n    // Initialize scores uniformly\n    const scores = new Map<string, number>();\n    const initialScore = 1 / n;\n    for (const node of nodes) {\n      scores.set(node.symbolId, initialScore);\n    }\n\n    // Precompute out-degree for each node\n    const outDegree = new Map<string, number>();\n    for (const node of nodes) {\n      outDegree.set(node.symbolId, graph.getForwardEdges(node.symbolId).length);\n    }\n\n    // Iterative PageRank\n    // Edge direction: A->B means \"A depends on B\" (A imports/calls/uses B)\n    // PageRank: B is important if many important nodes link to B\n    // Score distribution: each node distributes its score via forward edges to dependencies\n    // So we accumulate via reverse edges: for each node, sum score from nodes that point to it\n    let iterations = 0;\n    let converged = false;\n\n    while (iterations < maxIterations) {\n      const newScores = new Map<string, number>();\n      const base = (1 - damping) / n;\n\n      // Handle dangling nodes (no outgoing edges) — distribute their score evenly\n      let danglingSum = 0;\n      for (const node of nodes) {\n        if ((outDegree.get(node.symbolId) ?? 0) === 0) {\n          danglingSum += scores.get(node.symbolId) ?? 0;\n        }\n      }\n      const danglingContrib = damping * danglingSum / n;\n\n      for (const node of nodes) {\n        let incomingScore = 0;\n\n        // Sum contributions from all nodes that have a forward edge TO this node\n        // (i.e., reverse edges of this node)\n        const reverseEdges = graph.getReverseEdges(node.symbolId);\n        const contributors = new Set<string>();\n        for (const edge of reverseEdges) {\n          if (contributors.has(edge.from)) continue; // deduplicate multi-edges\n          contributors.add(edge.from);\n          const fromScore = scores.get(edge.from) ?? 0;\n          const fromOut = outDegree.get(edge.from) ?? 1;\n          incomingScore += fromScore / fromOut;\n        }\n\n        newScores.set(node.symbolId, base + damping * incomingScore + danglingContrib);\n      }\n\n      // Check convergence\n      let maxDelta = 0;\n      for (const node of nodes) {\n        const delta = Math.abs((newScores.get(node.symbolId) ?? 0) - (scores.get(node.symbolId) ?? 0));\n        if (delta > maxDelta) maxDelta = delta;\n      }\n\n      // Update scores\n      for (const [id, score] of newScores) {\n        scores.set(id, score);\n      }\n\n      iterations++;\n\n      if (maxDelta < tolerance) {\n        converged = true;\n        break;\n      }\n    }\n\n    // Build ranked results\n    const entries: PageRankEntry[] = nodes.map((node) => ({\n      symbolId: node.symbolId,\n      name: node.name,\n      kind: node.kind,\n      file: node.symbolId.split('::')[0] ?? '',\n      score: Math.round((scores.get(node.symbolId) ?? 0) * 1_000_000) / 1_000_000,\n      inDegree: graph.getReverseEdges(node.symbolId).length,\n      outDegree: outDegree.get(node.symbolId) ?? 0,\n    }));\n\n    // Sort by score descending\n    entries.sort((a, b) => b.score - a.score);\n\n    return {\n      rankings: entries.slice(0, limit),\n      totalSymbols: n,\n      iterations,\n      converged,\n    };\n  }\n}\n","import type { SymbolGraph } from '../graph/symbol-graph.js';\nimport type {\n  BoundaryViolation,\n  CommunityEntry,\n  CommunitySnapshot,\n} from '../types.js';\n\nexport interface BoundaryViolationDetectionResult {\n  readonly violations: BoundaryViolation[];\n  readonly confidence: 'high' | 'medium' | 'low';\n  readonly snapshotsAvailable: number;\n  readonly hint?: string;\n}\n\nconst HIGH_SEVERITY_THRESHOLD = 0;\nconst MEDIUM_SEVERITY_THRESHOLD = 2;\nconst MIN_SNAPSHOTS_FOR_CONFIDENCE = 2;\n\nexport class BoundaryViolationDetector {\n  detect(\n    graph: SymbolGraph,\n    current: CommunitySnapshot,\n    history: readonly CommunitySnapshot[],\n  ): BoundaryViolationDetectionResult {\n    const snapshotsAvailable = history.length;\n    const currentAssignments = assignmentMap(current.communities);\n    const currentLabels = labelMap(current.communities);\n    const historicalAssignments = history.map((snapshot) => ({\n      snapshot,\n      assignments: assignmentMap(snapshot.communities),\n      labels: labelMap(snapshot.communities),\n    }));\n\n    const violations: BoundaryViolation[] = [];\n\n    for (const edge of graph.allEdges()) {\n      if (edge.from === edge.to) continue;\n      const fromCommunity = currentAssignments.get(edge.from);\n      const toCommunity = currentAssignments.get(edge.to);\n      if (fromCommunity === undefined || toCommunity === undefined) continue;\n      if (fromCommunity === toCommunity) continue;\n\n      const fromLabel = currentLabels.get(fromCommunity) ?? `community-${fromCommunity}`;\n      const toLabel = currentLabels.get(toCommunity) ?? `community-${toCommunity}`;\n\n      const historicalCount =\n        snapshotsAvailable < MIN_SNAPSHOTS_FOR_CONFIDENCE\n          ? -1\n          : countHistoricalCrossCluster(historicalAssignments, edge.from, edge.to);\n\n      if (historicalCount === -1 || historicalCount <= MEDIUM_SEVERITY_THRESHOLD) {\n        violations.push({\n          from: {\n            symbolId: edge.from,\n            communityId: fromCommunity,\n            label: fromLabel,\n          },\n          to: {\n            symbolId: edge.to,\n            communityId: toCommunity,\n            label: toLabel,\n          },\n          edgeKind: edge.kind,\n          historicalEdgesBetweenClusters: historicalCount,\n          severity:\n            historicalCount === HIGH_SEVERITY_THRESHOLD ? 'high' : 'medium',\n        });\n      }\n    }\n\n    violations.sort((a, b) => {\n      if (a.severity !== b.severity) return a.severity === 'high' ? -1 : 1;\n      const cmp = a.from.symbolId.localeCompare(b.from.symbolId);\n      return cmp !== 0 ? cmp : a.to.symbolId.localeCompare(b.to.symbolId);\n    });\n\n    return {\n      violations,\n      confidence: confidenceFor(snapshotsAvailable),\n      snapshotsAvailable,\n      hint: hintFor(snapshotsAvailable),\n    };\n  }\n}\n\nfunction countHistoricalCrossCluster(\n  history: ReadonlyArray<{\n    readonly snapshot: CommunitySnapshot;\n    readonly assignments: ReadonlyMap<string, number>;\n    readonly labels: ReadonlyMap<number, string>;\n  }>,\n  fromSymbol: string,\n  toSymbol: string,\n): number {\n  let count = 0;\n  for (const snap of history) {\n    const fromId = snap.assignments.get(fromSymbol);\n    const toId = snap.assignments.get(toSymbol);\n    if (fromId === undefined || toId === undefined) continue;\n    if (fromId !== toId) count++;\n  }\n  return count;\n}\n\nfunction assignmentMap(entries: readonly CommunityEntry[]): Map<string, number> {\n  const map = new Map<string, number>();\n  for (const entry of entries) {\n    map.set(entry.symbolId, entry.communityId);\n  }\n  return map;\n}\n\nfunction labelMap(entries: readonly CommunityEntry[]): Map<number, string> {\n  const labels = new Map<number, string>();\n  for (const entry of entries) {\n    if (!labels.has(entry.communityId)) {\n      labels.set(entry.communityId, entry.communityLabel);\n    }\n  }\n  return labels;\n}\n\nfunction confidenceFor(snapshots: number): 'high' | 'medium' | 'low' {\n  if (snapshots >= 7) return 'high';\n  if (snapshots >= 3) return 'medium';\n  return 'low';\n}\n\nfunction hintFor(snapshots: number): string | undefined {\n  if (snapshots >= MIN_SNAPSHOTS_FOR_CONFIDENCE) return undefined;\n  return 'Insufficient snapshot history — enable `ctxo init` hook or add `ctxo index --check` to CI for boundary-violation signal.';\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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