ctxo-mcp 0.6.3 → 0.6.5

package/README.md

@@ -173,6 +173,8 @@ npx ctxo-mcp stats
 
 **Privacy Masking** AWS keys, GCP service accounts, Azure connection strings, JWTs, private IPs, env secrets automatically redacted. Extensible via `.ctxo/masking.json`.
 
+**Interactive Graph** `ctxo visualize` generates a self-contained HTML with vis.js dependency graph. ForceAtlas2 layout, PageRank-based sizing, layer coloring, blast radius on click, git history per symbol, dead code and anti-pattern filters, dark/light theme.
+
 **Debug Mode** `DEBUG=ctxo:*` for all debug output, or `DEBUG=ctxo:git,ctxo:storage` for specific namespaces.
 
 **Per-tool savings vs manual approach:**

package/dist/{chunk-WZKXGKKI.js → chunk-AXSQRYM3.js}

@@ -580,6 +580,92 @@ var SessionRecorderAdapter = class {
   }
 };
 
+// src/core/graph/symbol-graph.ts
+var SymbolGraph = class {
+  nodes = /* @__PURE__ */ new Map();
+  nodesByFileAndName = /* @__PURE__ */ new Map();
+  forwardEdges = /* @__PURE__ */ new Map();
+  reverseEdges = /* @__PURE__ */ new Map();
+  edgeSet = /* @__PURE__ */ new Set();
+  addNode(node) {
+    this.nodes.set(node.symbolId, node);
+    const [p0, p1] = node.symbolId.split("::");
+    if (p0 !== void 0 && p1 !== void 0) {
+      this.nodesByFileAndName.set(`${p0}::${p1}`, node);
+    }
+  }
+  addEdge(edge) {
+    const resolvedFrom = this.resolveNodeId(edge.from);
+    const resolvedTo = this.resolveNodeId(edge.to);
+    const resolvedEdge = { from: resolvedFrom, to: resolvedTo, kind: edge.kind };
+    const edgeKey = `${resolvedEdge.from}|${resolvedEdge.to}|${resolvedEdge.kind}`;
+    if (this.edgeSet.has(edgeKey)) return;
+    this.edgeSet.add(edgeKey);
+    const forward = this.forwardEdges.get(resolvedEdge.from) ?? [];
+    forward.push(resolvedEdge);
+    this.forwardEdges.set(resolvedEdge.from, forward);
+    const reverse = this.reverseEdges.get(resolvedEdge.to) ?? [];
+    reverse.push(resolvedEdge);
+    this.reverseEdges.set(resolvedEdge.to, reverse);
+  }
+  getNode(symbolId) {
+    return this.nodes.get(symbolId) ?? this.resolveNodeFuzzy(symbolId);
+  }
+  resolveNodeId(id) {
+    if (this.nodes.has(id)) return id;
+    const [p0, p1] = id.split("::");
+    if (p0 !== void 0 && p1 !== void 0) {
+      const fuzzyKey = `${p0}::${p1}`;
+      const match = this.nodesByFileAndName.get(fuzzyKey);
+      if (match) return match.symbolId;
+      const jsToTs = p0.replace(/\.js$/, ".ts");
+      if (jsToTs !== p0) {
+        const altKey = `${jsToTs}::${p1}`;
+        const altMatch = this.nodesByFileAndName.get(altKey);
+        if (altMatch) return altMatch.symbolId;
+      }
+    }
+    return id;
+  }
+  resolveNodeFuzzy(id) {
+    const [p0, p1] = id.split("::");
+    if (p0 !== void 0 && p1 !== void 0) {
+      const match = this.nodesByFileAndName.get(`${p0}::${p1}`);
+      if (match) return match;
+      const jsToTs = p0.replace(/\.js$/, ".ts");
+      if (jsToTs !== p0) {
+        return this.nodesByFileAndName.get(`${jsToTs}::${p1}`);
+      }
+    }
+    return void 0;
+  }
+  getForwardEdges(symbolId) {
+    return this.forwardEdges.get(symbolId) ?? [];
+  }
+  getReverseEdges(symbolId) {
+    return this.reverseEdges.get(symbolId) ?? [];
+  }
+  hasNode(symbolId) {
+    return this.nodes.has(symbolId) || this.resolveNodeFuzzy(symbolId) !== void 0;
+  }
+  get nodeCount() {
+    return this.nodes.size;
+  }
+  get edgeCount() {
+    return this.edgeSet.size;
+  }
+  allNodes() {
+    return [...this.nodes.values()];
+  }
+  allEdges() {
+    const edges = [];
+    for (const list of this.forwardEdges.values()) {
+      edges.push(...list);
+    }
+    return edges;
+  }
+};
+
 // src/core/why-context/revert-detector.ts
 var REVERT_QUOTED_PATTERN = /^Revert "(.+)"$/;
 var REVERT_PREFIX_PATTERN = /^revert:\s*(.+)$/i;
@@ -619,6 +705,345 @@ var RevertDetector = class {
   }
 };
 
+// src/core/overlay/architectural-overlay.ts
+var DEFAULT_RULES = [
+  // Test layer (matched first — __tests__, .test.ts, tests/, fixtures)
+  { pattern: /__tests__/, layer: "Test" },
+  { pattern: /\.test\.ts$/, layer: "Test" },
+  { pattern: /\btests\b/, layer: "Test" },
+  { pattern: /\bfixtures?\b/, layer: "Test" },
+  // Composition root
+  { pattern: /src\/index\.ts$/, layer: "Composition" },
+  // Domain
+  { pattern: /\bcore\b/, layer: "Domain" },
+  { pattern: /\bports?\b/, layer: "Domain" },
+  // Adapter
+  { pattern: /\badapters?\b/, layer: "Adapter" },
+  { pattern: /\bcli\b/, layer: "Adapter" },
+  // Infrastructure
+  { pattern: /\binfra\b/, layer: "Infrastructure" },
+  { pattern: /\bdb\b/, layer: "Infrastructure" },
+  { pattern: /\bqueue\b/, layer: "Infrastructure" },
+  // Config files
+  { pattern: /\.(config|rc)\.(ts|js|json)$/, layer: "Configuration" }
+];
+var ArchitecturalOverlay = class {
+  rules;
+  constructor(customRules) {
+    this.rules = (customRules ?? DEFAULT_RULES).map(({ pattern, layer }) => ({
+      pattern: new RegExp(pattern.source, pattern.flags),
+      layer
+    }));
+  }
+  classify(filePaths) {
+    const layers = {};
+    for (const filePath of filePaths) {
+      const layer = this.matchLayer(filePath);
+      const list = layers[layer] ?? [];
+      list.push(filePath);
+      layers[layer] = list;
+    }
+    return { layers };
+  }
+  matchLayer(filePath) {
+    for (const rule of this.rules) {
+      if (rule.pattern.test(filePath)) {
+        return rule.layer;
+      }
+    }
+    return "Unknown";
+  }
+};
+
+// src/core/dead-code/dead-code-detector.ts
+var TEST_PATTERNS = [/__tests__/, /\.test\.ts$/, /\.spec\.ts$/, /\btests\//, /\bfixtures?\//];
+var CONFIG_PATTERNS = [/\.(config|rc)\.(ts|js|json)$/, /tsconfig/, /eslint/, /\.d\.ts$/];
+var FRAMEWORK_PATTERNS = [
+  // Vitest
+  /^(describe|it|expect|beforeAll|beforeEach|afterAll|afterEach|vi)$/,
+  // MCP SDK
+  /^(registerTool|registerPrompt|connect|close)$/,
+  // Zod schemas (conventionally exported for validation)
+  /Schema$/,
+  // Node.js lifecycle
+  /^main$/
+];
+var SCAFFOLDING_PATTERNS = [
+  { regex: /\bTODO\b/i, pattern: "TODO" },
+  { regex: /\bFIXME\b/i, pattern: "FIXME" },
+  { regex: /\bHACK\b/i, pattern: "HACK" },
+  { regex: /\bPLACEHOLDER\b/i, pattern: "PLACEHOLDER" },
+  { regex: /\bXXX\b/, pattern: "XXX" },
+  { regex: /Phase\s+\d|Step\s+\d/i, pattern: "PHASE/STEP" },
+  { regex: /not\s+(?:yet\s+)?implement/i, pattern: "NOT_IMPLEMENTED" },
+  { regex: /temporary|temp\s+fix/i, pattern: "TEMPORARY" }
+];
+var DeadCodeDetector = class {
+  detect(graph, options = {}) {
+    const allNodes = graph.allNodes();
+    const candidates = options.includeTests ? allNodes : allNodes.filter((n) => {
+      const file = n.symbolId.split("::")[0] ?? "";
+      return !this.matchesAny(file, TEST_PATTERNS) && !this.matchesAny(file, CONFIG_PATTERNS);
+    });
+    if (candidates.length === 0) {
+      return { totalSymbols: 0, reachableSymbols: 0, deadSymbols: [], unusedExports: [], deadFiles: [], scaffolding: this.detectScaffolding(options.sourceContents), deadCodePercentage: 0 };
+    }
+    const candidateIds = new Set(candidates.map((n) => n.symbolId));
+    const entryPoints = /* @__PURE__ */ new Set();
+    for (const node of candidates) {
+      if (this.isFrameworkSymbol(node.name)) {
+        entryPoints.add(node.symbolId);
+        continue;
+      }
+      const reverseEdges = graph.getReverseEdges(node.symbolId);
+      const forwardEdges = graph.getForwardEdges(node.symbolId);
+      const incomingFromCandidates = reverseEdges.filter((e) => candidateIds.has(e.from) && e.from !== node.symbolId);
+      if (incomingFromCandidates.length === 0) {
+        const hasOutgoing = forwardEdges.some((e) => candidateIds.has(e.to));
+        if (hasOutgoing || reverseEdges.length > 0) {
+          entryPoints.add(node.symbolId);
+        }
+      }
+    }
+    const reachable = /* @__PURE__ */ new Set();
+    const queue = [...entryPoints];
+    while (queue.length > 0) {
+      const current = queue.shift();
+      if (reachable.has(current)) continue;
+      reachable.add(current);
+      for (const edge of graph.getForwardEdges(current)) {
+        if (!reachable.has(edge.to) && candidateIds.has(edge.to)) {
+          queue.push(edge.to);
+        }
+      }
+    }
+    const deadIds = /* @__PURE__ */ new Set();
+    for (const node of candidates) {
+      if (!reachable.has(node.symbolId)) {
+        deadIds.add(node.symbolId);
+      }
+    }
+    const cascadeDepthMap = this.computeCascadeDepths(graph, deadIds, candidateIds);
+    const deadSymbols = [];
+    for (const node of candidates) {
+      if (!deadIds.has(node.symbolId)) continue;
+      const file = node.symbolId.split("::")[0] ?? "";
+      const confidence = this.computeConfidence(graph, node.symbolId, deadIds);
+      const cascadeDepth = cascadeDepthMap.get(node.symbolId);
+      deadSymbols.push({
+        symbolId: node.symbolId,
+        file,
+        name: node.name,
+        kind: node.kind,
+        confidence,
+        reason: this.describeReason(confidence),
+        ...cascadeDepth !== void 0 && cascadeDepth > 0 ? { cascadeDepth } : {}
+      });
+    }
+    const fileStats = /* @__PURE__ */ new Map();
+    for (const node of candidates) {
+      const file = node.symbolId.split("::")[0] ?? "";
+      const stats = fileStats.get(file) ?? { total: 0, dead: 0 };
+      stats.total++;
+      if (deadIds.has(node.symbolId)) stats.dead++;
+      fileStats.set(file, stats);
+    }
+    const deadFiles = [...fileStats.entries()].filter(([, s]) => s.total > 0 && s.dead === s.total).map(([file]) => file);
+    const unusedExports = [];
+    for (const node of candidates) {
+      const reverseEdges = graph.getReverseEdges(node.symbolId);
+      const externalImporters = reverseEdges.filter(
+        (e) => candidateIds.has(e.from) && e.from !== node.symbolId
+      );
+      if (externalImporters.length === 0 && !deadIds.has(node.symbolId)) {
+        unusedExports.push({
+          symbolId: node.symbolId,
+          file: node.symbolId.split("::")[0] ?? "",
+          name: node.name,
+          kind: node.kind
+        });
+      }
+    }
+    const scaffolding = this.detectScaffolding(options.sourceContents);
+    const deadCodePercentage = Math.round(deadSymbols.length / candidates.length * 100 * 10) / 10;
+    return {
+      totalSymbols: candidates.length,
+      reachableSymbols: reachable.size,
+      deadSymbols,
+      unusedExports,
+      deadFiles,
+      scaffolding,
+      deadCodePercentage
+    };
+  }
+  computeConfidence(graph, symbolId, deadIds) {
+    const reverseEdges = graph.getReverseEdges(symbolId);
+    if (reverseEdges.length === 0) {
+      return 1;
+    }
+    const allImportersExcluded = reverseEdges.every((e) => {
+      const importerFile = e.from.split("::")[0] ?? "";
+      return this.matchesAny(importerFile, TEST_PATTERNS) || this.matchesAny(importerFile, CONFIG_PATTERNS);
+    });
+    if (allImportersExcluded) {
+      return 0.9;
+    }
+    const allImportersDead = reverseEdges.every((e) => deadIds.has(e.from));
+    if (allImportersDead) {
+      return 0.7;
+    }
+    return 0.7;
+  }
+  describeReason(confidence) {
+    switch (confidence) {
+      case 1:
+        return "Zero importers \u2014 no code references this symbol";
+      case 0.9:
+        return "Only referenced from test/config files";
+      case 0.7:
+        return "All importers are themselves dead (cascading)";
+    }
+  }
+  isFrameworkSymbol(name) {
+    return FRAMEWORK_PATTERNS.some((p) => p.test(name));
+  }
+  computeCascadeDepths(graph, deadIds, candidateIds) {
+    const depths = /* @__PURE__ */ new Map();
+    const rootDead = /* @__PURE__ */ new Set();
+    for (const id of deadIds) {
+      const reverseEdges = graph.getReverseEdges(id);
+      const deadImporters = reverseEdges.filter((e) => deadIds.has(e.from) && e.from !== id);
+      if (deadImporters.length === 0) {
+        rootDead.add(id);
+        depths.set(id, 0);
+      }
+    }
+    const queue = [...rootDead].map((id) => ({ id, depth: 0 }));
+    const visited = new Set(rootDead);
+    while (queue.length > 0) {
+      const current = queue.shift();
+      for (const edge of graph.getForwardEdges(current.id)) {
+        if (deadIds.has(edge.to) && !visited.has(edge.to) && candidateIds.has(edge.to)) {
+          const newDepth = current.depth + 1;
+          depths.set(edge.to, newDepth);
+          visited.add(edge.to);
+          queue.push({ id: edge.to, depth: newDepth });
+        }
+      }
+    }
+    return depths;
+  }
+  detectScaffolding(sourceContents) {
+    if (!sourceContents || sourceContents.size === 0) return [];
+    const results = [];
+    for (const [file, content] of sourceContents) {
+      if (this.matchesAny(file, TEST_PATTERNS) || this.matchesAny(file, CONFIG_PATTERNS)) continue;
+      const lines = content.split("\n");
+      for (let i = 0; i < lines.length; i++) {
+        const line = lines[i];
+        for (const { regex, pattern } of SCAFFOLDING_PATTERNS) {
+          if (regex.test(line)) {
+            results.push({
+              file,
+              line: i + 1,
+              pattern,
+              text: line.trim().slice(0, 120)
+            });
+            break;
+          }
+        }
+      }
+    }
+    return results;
+  }
+  matchesAny(value, patterns) {
+    return patterns.some((p) => p.test(value));
+  }
+};
+
+// src/core/importance/pagerank-calculator.ts
+var DEFAULT_DAMPING = 0.85;
+var DEFAULT_MAX_ITERATIONS = 100;
+var DEFAULT_TOLERANCE = 1e-6;
+var DEFAULT_LIMIT = 25;
+var PageRankCalculator = class {
+  calculate(graph, options = {}) {
+    const damping = options.damping ?? DEFAULT_DAMPING;
+    const maxIterations = options.maxIterations ?? DEFAULT_MAX_ITERATIONS;
+    const tolerance = options.tolerance ?? DEFAULT_TOLERANCE;
+    const limit = options.limit ?? DEFAULT_LIMIT;
+    const nodes = graph.allNodes();
+    const n = nodes.length;
+    if (n === 0) {
+      return { rankings: [], totalSymbols: 0, iterations: 0, converged: true };
+    }
+    const scores = /* @__PURE__ */ new Map();
+    const initialScore = 1 / n;
+    for (const node of nodes) {
+      scores.set(node.symbolId, initialScore);
+    }
+    const outDegree = /* @__PURE__ */ new Map();
+    for (const node of nodes) {
+      outDegree.set(node.symbolId, graph.getForwardEdges(node.symbolId).length);
+    }
+    let iterations = 0;
+    let converged = false;
+    while (iterations < maxIterations) {
+      const newScores = /* @__PURE__ */ new Map();
+      const base = (1 - damping) / n;
+      let danglingSum = 0;
+      for (const node of nodes) {
+        if ((outDegree.get(node.symbolId) ?? 0) === 0) {
+          danglingSum += scores.get(node.symbolId) ?? 0;
+        }
+      }
+      const danglingContrib = damping * danglingSum / n;
+      for (const node of nodes) {
+        let incomingScore = 0;
+        const reverseEdges = graph.getReverseEdges(node.symbolId);
+        const contributors = /* @__PURE__ */ new Set();
+        for (const edge of reverseEdges) {
+          if (contributors.has(edge.from)) continue;
+          contributors.add(edge.from);
+          const fromScore = scores.get(edge.from) ?? 0;
+          const fromOut = outDegree.get(edge.from) ?? 1;
+          incomingScore += fromScore / fromOut;
+        }
+        newScores.set(node.symbolId, base + damping * incomingScore + danglingContrib);
+      }
+      let maxDelta = 0;
+      for (const node of nodes) {
+        const delta = Math.abs((newScores.get(node.symbolId) ?? 0) - (scores.get(node.symbolId) ?? 0));
+        if (delta > maxDelta) maxDelta = delta;
+      }
+      for (const [id, score] of newScores) {
+        scores.set(id, score);
+      }
+      iterations++;
+      if (maxDelta < tolerance) {
+        converged = true;
+        break;
+      }
+    }
+    const entries = nodes.map((node) => ({
+      symbolId: node.symbolId,
+      name: node.name,
+      kind: node.kind,
+      file: node.symbolId.split("::")[0] ?? "",
+      score: Math.round((scores.get(node.symbolId) ?? 0) * 1e6) / 1e6,
+      inDegree: graph.getReverseEdges(node.symbolId).length,
+      outDegree: outDegree.get(node.symbolId) ?? 0
+    }));
+    entries.sort((a, b) => b.score - a.score);
+    return {
+      rankings: entries.slice(0, limit),
+      totalSymbols: n,
+      iterations,
+      converged
+    };
+  }
+};
+
 // src/core/co-change/co-change-analyzer.ts
 var MIN_SHARED_COMMITS = 2;
 var MIN_FREQUENCY = 0.1;
@@ -693,10 +1118,14 @@ function loadCoChangeMap(matrix) {
 export {
   createLogger,
   SqliteStorageAdapter,
+  SymbolGraph,
   RevertDetector,
   SimpleGitAdapter,
+  ArchitecturalOverlay,
+  DeadCodeDetector,
+  PageRankCalculator,
   aggregateCoChanges,
   loadCoChangeMap,
   SessionRecorderAdapter
 };
-//# sourceMappingURL=chunk-WZKXGKKI.js.map
+//# sourceMappingURL=chunk-AXSQRYM3.js.map

package/dist/chunk-AXSQRYM3.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/logger.ts","../src/adapters/storage/sqlite-storage-adapter.ts","../src/adapters/git/simple-git-adapter.ts","../src/adapters/stats/session-recorder-adapter.ts","../src/core/graph/symbol-graph.ts","../src/core/why-context/revert-detector.ts","../src/core/overlay/architectural-overlay.ts","../src/core/dead-code/dead-code-detector.ts","../src/core/importance/pagerank-calculator.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    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  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 { 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: ${(err as Error).message}`);\n    }\n  }\n}\n","import type { SymbolNode, GraphEdge } from '../types.js';\n\nexport class SymbolGraph {\n  private readonly nodes = new Map<string, SymbolNode>();\n  private readonly nodesByFileAndName = new Map<string, SymbolNode>();\n  private readonly forwardEdges = new Map<string, GraphEdge[]>();\n  private readonly reverseEdges = new Map<string, GraphEdge[]>();\n  private edgeSet = new Set<string>();\n\n  addNode(node: SymbolNode): void {\n    this.nodes.set(node.symbolId, node);\n    // Index by file::name (ignoring kind) for fuzzy edge resolution\n    const [p0, p1] = node.symbolId.split('::');\n    if (p0 !== undefined && p1 !== undefined) {\n      this.nodesByFileAndName.set(`${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","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 { 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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