ctxo-mcp 0.2.0 → 0.3.1

package/README.md

@@ -0,0 +1,188 @@
+# Ctxo
+
+**Code intelligence for AI agents — one call instead of hundreds.**
+
+AI coding assistants waste context window reading files one by one, still missing dependencies. Ctxo gives them the full picture in a single MCP call: symbol graphs, blast radius, git intent, and risk scores.
+
+```
+Context per query set (full codebase investigation):
+
+Manual   ████████████████████████████████████████  140,000 tokens
+Ctxo     █░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░    2,900 tokens  → 48x less
+
+Tool calls per query set:
+
+Manual   ████████████████████████████████████████  409+ calls
+Ctxo     █░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░    8 calls       → 51x fewer
+
+Context after 10 investigation rounds:
+
+Manual   ██████████████████████████████████████████ 140% — OOM at round 7
+Ctxo     █░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░ 2.9% — 97% free for coding
+```
+
+## Quick Start
+
+```Shell
+# 1. Index your codebase
+npx ctxo-mcp index
+
+# 2. Add to your IDE's MCP config
+# (see IDE Setup below)
+
+# 3. Start using — your AI assistant now has 14 code intelligence tools
+```
+
+## IDE Setup
+
+**Claude Code / Cursor / Windsurf / Cline** — `.mcp.json`:
+
+```JSON
+{ "mcpServers": { "ctxo": { "command": "npx", "args": ["-y", "ctxo-mcp"] } } }
+```
+
+**VS Code (Copilot)** — `.vscode/mcp.json`:
+
+```JSON
+{ "servers": { "ctxo": { "type": "stdio", "command": "npx", "args": ["-y", "ctxo-mcp"] } } }
+```
+
+**Zed** — `settings.json`:
+
+```JSON
+{ "context_servers": { "ctxo": { "command": { "path": "npx", "args": ["-y", "ctxo-mcp"] } } } }
+```
+
+## 14 Tools
+
+| Tool                        | What it does                                                     |
+| --------------------------- | ---------------------------------------------------------------- |
+| `get_logic_slice`           | Symbol + transitive dependencies (L1-L4 progressive detail)      |
+| `get_blast_radius`          | What breaks if this changes (3-tier: confirmed/likely/potential) |
+| `get_architectural_overlay` | Project layer map (Domain/Infrastructure/Adapter)                |
+| `get_why_context`           | Git commit intent + anti-pattern warnings (reverts, rollbacks)   |
+| `get_change_intelligence`   | Complexity x churn composite score                               |
+| `find_dead_code`            | Unreachable symbols, unused exports, scaffolding markers         |
+| `get_context_for_task`      | Task-optimized context (fix/extend/refactor/understand)          |
+| `get_ranked_context`        | BM25 + PageRank search within token budget                       |
+| `search_symbols`            | Symbol name/regex search across index                            |
+| `get_changed_symbols`       | Symbols in recently changed files (git diff)                     |
+| `find_importers`            | Reverse dependency lookup ("who uses this?")                     |
+| `get_class_hierarchy`       | Class inheritance tree (ancestors + descendants)                 |
+| `get_symbol_importance`     | PageRank centrality ranking                                      |
+| `get_pr_impact`             | Full PR risk assessment in a single call                         |
+
+## Tool Selection Guide
+
+```
+Reviewing a PR?           → get_pr_impact
+About to modify code?     → get_blast_radius → get_why_context
+Understanding a symbol?   → get_context_for_task(taskType: "understand")
+Fixing a bug?             → get_context_for_task(taskType: "fix")
+Refactoring?              → get_context_for_task(taskType: "refactor")
+Don't know the name?      → search_symbols or get_ranked_context
+Finding unused code?      → find_dead_code
+Safe to delete?           → find_importers
+Onboarding?               → get_architectural_overlay → get_symbol_importance
+```
+
+## CLI Commands
+
+```Shell
+npx ctxo-mcp index                # Build full codebase index
+npx ctxo-mcp index --check        # CI gate: fail if index stale
+npx ctxo-mcp index --skip-history # Fast re-index without git history
+npx ctxo-mcp watch                # File watcher for incremental re-index
+npx ctxo-mcp init                 # Install git hooks (post-commit, post-merge)
+npx ctxo-mcp status               # Show index manifest
+npx ctxo-mcp sync                 # Rebuild SQLite cache from committed JSON
+```
+
+## Features
+
+**Response Envelope** — All responses include `_meta` with item counts, truncation info, and drill-in hints. Large results auto-truncated at 8KB (configurable via `CTXO_RESPONSE_LIMIT`).
+
+**Intent Filtering** — 4 tools accept `intent` parameter for keyword-based result filtering. `get_blast_radius(symbolId, intent: "test")` returns only test-related impacts.
+
+**Tool Annotations** — All tools declare `readOnlyHint: true`, `idempotentHint: true`, `openWorldHint: false` for safe auto-approval in agent frameworks.
+
+**Privacy Masking** — AWS keys, GCP service accounts, Azure connection strings, JWTs, private IPs, env secrets automatically redacted. Extensible via `.ctxo/masking.json`.
+
+**Debug Mode** — `DEBUG=ctxo:*` for all debug output, or `DEBUG=ctxo:git,ctxo:storage` for specific namespaces.
+
+**Per-tool savings vs manual approach:**
+
+```
+                        Manual Tokens   Ctxo Tokens   Savings
+get_logic_slice         ████████ 1,950  █ 150         92%
+get_blast_radius        ███ 800         ██ 600        25%
+get_overlay             ████████████ 25K██ 500        98%
+get_why_context         █ 200           █ 200          0%
+get_change_intelligence ████████ 2,100  ▏ 50          98%
+find_dead_code          █████████ 5,000 ████ 2,000    60%
+────────────────────────────────────────────────────────────
+TOTAL                   35,050 tokens   3,500 tokens  90%
+                        329+ calls      6 calls       98%
+```
+
+## Agentic AI Usage
+
+**Claude Agent SDK:**
+
+```TypeScript
+import { query } from "@anthropic-ai/claude-agent-sdk";
+
+for await (const message of query({
+  prompt: "Analyze the blast radius of AuthService",
+  options: {
+    mcpServers: { ctxo: { command: "npx", args: ["-y", "ctxo-mcp"] } },
+    allowedTools: ["mcp__ctxo__*"]
+  }
+})) { /* ... */ }
+```
+
+**OpenAI Agents SDK:**
+
+```Python
+from agents import Agent, Runner
+from agents.mcp import MCPServerStdio
+
+async with MCPServerStdio(params={"command": "npx", "args": ["ctxo-mcp"]}) as ctxo:
+    agent = Agent(name="Reviewer", mcp_servers=[ctxo])
+    result = await Runner.run(agent, "Review the PR impact")
+```
+
+See [Agentic AI Integration Guide](docs/agentic-ai-integration.md) for LangChain, raw MCP client, and CI/CD examples.
+
+## Multi-Language Support
+
+| Language              | Parser      | Tier   | Features                                                         |
+| --------------------- | ----------- | ------ | ---------------------------------------------------------------- |
+| TypeScript/JavaScript | ts-morph    | Full   | Type-aware resolution, cross-file imports, `this.method()` calls |
+| Go                    | tree-sitter | Syntax | Structs, interfaces, functions, methods, import edges            |
+| C#                    | tree-sitter | Syntax | Classes, interfaces, methods, enums, namespace qualification     |
+
+## How It Works
+
+Ctxo builds a **committed JSON index** (`.ctxo/index/`) that captures symbols, dependency edges, git history, and co-change data. The MCP server reads this index to answer queries — no runtime parsing, no external services.
+
+```
+.ctxo/
+  index/          ← committed (per-file JSON, reviewable in PRs)
+  .cache/         ← gitignored (local SQLite, auto-rebuilt)
+  config.yaml     ← committed (team settings)
+  masking.json    ← committed (custom masking patterns)
+```
+
+## Links
+
+* [npm](https://www.npmjs.com/package/ctxo-mcp)
+* [Changelog](CHANGELOG.md)
+* [LLM Reference](llms-full.txt)
+* [Validation Runbook](docs/runbook/mcp-validation/mcp-validation.md)
+* [Architecture](docs/artifacts/architecture.md)
+* [PRD](docs/artifacts/prd.md)
+
+## License
+
+MIT

package/dist/chunk-JIDIH7DS.js

@@ -0,0 +1,28 @@
+#!/usr/bin/env node
+var __defProp = Object.defineProperty;
+var __getOwnPropDesc = Object.getOwnPropertyDescriptor;
+var __getOwnPropNames = Object.getOwnPropertyNames;
+var __hasOwnProp = Object.prototype.hasOwnProperty;
+var __esm = (fn, res) => function __init() {
+  return fn && (res = (0, fn[__getOwnPropNames(fn)[0]])(fn = 0)), res;
+};
+var __export = (target, all) => {
+  for (var name in all)
+    __defProp(target, name, { get: all[name], enumerable: true });
+};
+var __copyProps = (to, from, except, desc) => {
+  if (from && typeof from === "object" || typeof from === "function") {
+    for (let key of __getOwnPropNames(from))
+      if (!__hasOwnProp.call(to, key) && key !== except)
+        __defProp(to, key, { get: () => from[key], enumerable: !(desc = __getOwnPropDesc(from, key)) || desc.enumerable });
+  }
+  return to;
+};
+var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: true }), mod);
+
+export {
+  __esm,
+  __export,
+  __toCommonJS
+};
+//# sourceMappingURL=chunk-JIDIH7DS.js.map

package/dist/{chunk-54ETLIQX.js → chunk-N6GPODUY.js}

@@ -44,14 +44,17 @@ var SymbolNodeSchema = z.object({
   name: z.string().min(1),
   kind: SymbolKindSchema,
   startLine: z.number().int().nonnegative(),
-  endLine: z.number().int().nonnegative()
+  endLine: z.number().int().nonnegative(),
+  startOffset: z.number().int().nonnegative().optional(),
+  endOffset: z.number().int().nonnegative().optional()
 }).refine((node) => node.endLine >= node.startLine, {
   message: "endLine must be >= startLine"
 });
 var GraphEdgeSchema = z.object({
   from: SymbolIdSchema,
   to: SymbolIdSchema,
-  kind: EdgeKindSchema
+  kind: EdgeKindSchema,
+  typeOnly: z.boolean().optional()
 });
 var CommitIntentSchema = z.object({
   hash: z.string().min(1),
@@ -130,7 +133,7 @@ var JsonIndexReader = class {
       const fullPath = join(dir, entry.name);
       if (entry.isDirectory()) {
         files.push(...this.collectJsonFiles(fullPath, visited));
-      } else if (entry.name.endsWith(".json")) {
+      } else if (entry.name.endsWith(".json") && entry.name !== "co-changes.json") {
         files.push(fullPath);
       }
     }
@@ -139,7 +142,8 @@ var JsonIndexReader = class {
 };
 
 export {
+  SYMBOL_KINDS,
   DetailLevelSchema,
   JsonIndexReader
 };
-//# sourceMappingURL=chunk-54ETLIQX.js.map
+//# sourceMappingURL=chunk-N6GPODUY.js.map

package/dist/chunk-N6GPODUY.js.map

@@ -0,0 +1 @@
+{"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 entirely\n\n      const fullPath = join(dir, entry.name);\n      if (entry.isDirectory()) {\n        files.push(...this.collectJsonFiles(fullPath, visited));\n      } else if (entry.name.endsWith('.json') && entry.name !== 'co-changes.json') {\n        files.push(fullPath);\n      }\n    }\n\n    return files;\n  }\n}\n","import { z } from 'zod';\n\n// ── Symbol Kinds ────────────────────────────────────────────────\n\nexport const SYMBOL_KINDS = [\n  'function',\n  'class',\n  'interface',\n  'method',\n  'variable',\n  'type',\n] as const;\n\nexport const SymbolKindSchema = z.enum(SYMBOL_KINDS);\nexport type SymbolKind = z.infer<typeof SymbolKindSchema>;\n\n// ── Edge Kinds ──────────────────────────────────────────────────\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  contentHash: z.string().optional(),\n  symbols: z.array(SymbolNodeSchema),\n  edges: z.array(GraphEdgeSchema),\n  complexity: z.array(ComplexityMetricsSchema).optional(),\n  intent: z.array(CommitIntentSchema),\n  antiPatterns: z.array(AntiPatternSchema),\n});\nexport type FileIndex = z.infer<typeof FileIndexSchema>;\n\n// ── Logic-Slice Result ──────────────────────────────────────────\n\nexport interface LogicSliceResult {\n  readonly root: SymbolNode;\n  readonly dependencies: readonly SymbolNode[];\n  readonly edges: readonly GraphEdge[];\n}\n\n// ── Formatted Slice ─────────────────────────────────────────────\n\nexport interface TruncationInfo {\n  readonly truncated: true;\n  readonly reason: 'token_budget_exceeded';\n}\n\nexport interface FormattedSlice {\n  readonly root: SymbolNode;\n  readonly dependencies: readonly SymbolNode[];\n  readonly edges: readonly GraphEdge[];\n  readonly level: DetailLevel;\n  readonly levelDescription?: string;\n  readonly truncation?: 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  readonly file1: string;\n  readonly file2: string;\n  readonly sharedCommits: number;\n  readonly frequency: number;\n}\n\nexport interface CoChangeMatrix {\n  readonly version: 1;\n  readonly timestamp: number;\n  readonly entries: readonly CoChangeEntry[];\n}\n\n// ── Commit Record (from git adapter) ────────────────────────────\n\nexport interface CommitRecord {\n  readonly hash: string;\n  readonly message: string;\n  readonly date: string;\n  readonly author: string;\n}\n\n// ── Blame Line (from git adapter) ───────────────────────────────\n\nexport interface BlameLine {\n  readonly hash: string;\n  readonly lineNumber: number;\n  readonly author: string;\n  readonly date: 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package/dist/{chunk-P7JUSY3I.js → chunk-XSHNN6PU.js}

@@ -1,12 +1,45 @@
 #!/usr/bin/env node
 import {
   JsonIndexReader
-} from "./chunk-54ETLIQX.js";
+} from "./chunk-N6GPODUY.js";
+
+// src/core/logger.ts
+function isDebugEnabled(namespace) {
+  const debugEnv = process.env["DEBUG"] ?? "";
+  if (!debugEnv) return false;
+  const patterns = debugEnv.split(",").map((p) => p.trim());
+  return patterns.some((p) => {
+    if (p === "*" || p === "ctxo:*") return true;
+    if (p === namespace) return true;
+    if (p.endsWith(":*") && namespace.startsWith(p.slice(0, -1))) return true;
+    return false;
+  });
+}
+function createLogger(namespace) {
+  const prefix = `[${namespace}]`;
+  return {
+    debug(message, ...args) {
+      if (isDebugEnabled(namespace)) {
+        console.error(`${prefix} DEBUG ${message}`, ...args);
+      }
+    },
+    info(message, ...args) {
+      console.error(`${prefix} ${message}`, ...args);
+    },
+    warn(message, ...args) {
+      console.error(`${prefix} WARN ${message}`, ...args);
+    },
+    error(message, ...args) {
+      console.error(`${prefix} ERROR ${message}`, ...args);
+    }
+  };
+}
 
 // src/adapters/storage/sqlite-storage-adapter.ts
 import initSqlJs from "sql.js";
 import { readFileSync, writeFileSync, existsSync, mkdirSync } from "fs";
 import { join, dirname } from "path";
+var log = createLogger("ctxo:storage");
 var SqliteStorageAdapter = class {
   db;
   dbPath;
@@ -23,16 +56,15 @@ var SqliteStorageAdapter = class {
         this.db = new SQL.Database(buffer);
         this.verifyIntegrity();
       } catch {
-        console.error("[ctxo:sqlite] Corrupt DB detected, rebuilding from JSON index");
+        log.warn("Corrupt DB detected, rebuilding from JSON index");
         this.db = new SQL.Database();
         this.createTables();
-        this.rebuildFromJson();
       }
     } else {
       this.db = new SQL.Database();
       this.createTables();
-      this.rebuildFromJson();
     }
+    this.rebuildFromJson();
   }
   async initEmpty() {
     const SQL = await initSqlJs();
@@ -107,7 +139,7 @@ var SqliteStorageAdapter = class {
       );
       for (const sym of fileIndex.symbols) {
         db.run(
-          "INSERT INTO symbols (symbol_id, name, kind, file_path, start_line, end_line) VALUES (?, ?, ?, ?, ?, ?)",
+          "INSERT OR REPLACE INTO symbols (symbol_id, name, kind, file_path, start_line, end_line) VALUES (?, ?, ?, ?, ?, ?)",
           [sym.symbolId, sym.name, sym.kind, fileIndex.file, sym.startLine, sym.endLine]
         );
       }
@@ -238,7 +270,7 @@ var SqliteStorageAdapter = class {
         );
         for (const sym of fileIndex.symbols) {
           db.run(
-            "INSERT INTO symbols (symbol_id, name, kind, file_path, start_line, end_line) VALUES (?, ?, ?, ?, ?, ?)",
+            "INSERT OR REPLACE INTO symbols (symbol_id, name, kind, file_path, start_line, end_line) VALUES (?, ?, ?, ?, ?, ?)",
             [sym.symbolId, sym.name, sym.kind, fileIndex.file, sym.startLine, sym.endLine]
           );
         }
@@ -274,7 +306,7 @@ var SqliteStorageAdapter = class {
     try {
       this.persist();
     } catch (err) {
-      console.error(`[ctxo:sqlite] Failed to persist DB: ${err.message}`);
+      log.error(`Failed to persist DB: ${err.message}`);
     }
   }
   deleteFileData(db, filePath) {
@@ -322,10 +354,12 @@ var SqliteStorageAdapter = class {
 
 // src/adapters/git/simple-git-adapter.ts
 import { simpleGit } from "simple-git";
+var log2 = createLogger("ctxo:git");
 var SimpleGitAdapter = class {
   git;
   constructor(projectRoot) {
     this.git = simpleGit(projectRoot);
+    log2.debug("Initialized with root: %s", projectRoot);
   }
   async isAvailable() {
     try {
@@ -335,29 +369,72 @@ var SimpleGitAdapter = class {
       return false;
     }
   }
-  async getCommitHistory(filePath) {
+  async getCommitHistory(filePath, maxCount) {
     try {
-      const log = await this.git.log({ file: filePath, "--follow": null });
-      return log.all.map((entry) => ({
+      const log3 = await this.git.log({
+        file: filePath,
+        "--follow": null,
+        ...maxCount ? { maxCount } : {}
+      });
+      return log3.all.map((entry) => ({
         hash: entry.hash,
         message: entry.message,
         date: entry.date,
         author: entry.author_name
       }));
     } catch (err) {
-      console.error(`[ctxo:git] Failed to get history for ${filePath}: ${err.message}`);
+      log2.error(` Failed to get history for ${filePath}: ${err.message}`);
+      return [];
+    }
+  }
+  async getBatchHistory(maxCount = 20) {
+    try {
+      const log3 = await this.git.log({ maxCount: maxCount * 50, "--name-only": null });
+      const result = /* @__PURE__ */ new Map();
+      for (const entry of log3.all) {
+        const record = {
+          hash: entry.hash,
+          message: entry.message,
+          date: entry.date,
+          author: entry.author_name
+        };
+        const diff = entry.diff;
+        const files = diff?.files?.map((f) => f.file.replace(/\\/g, "/")) ?? [];
+        for (const file of files) {
+          let list = result.get(file);
+          if (!list) {
+            list = [];
+            result.set(file, list);
+          }
+          if (list.length < maxCount) {
+            list.push(record);
+          }
+        }
+      }
+      return result;
+    } catch (err) {
+      log2.error(` Batch history failed: ${err.message}`);
+      return /* @__PURE__ */ new Map();
+    }
+  }
+  async getChangedFiles(since) {
+    try {
+      const diff = await this.git.diffSummary([since]);
+      return diff.files.map((f) => f.file.replace(/\\/g, "/"));
+    } catch (err) {
+      log2.error(` Failed to get changed files since ${since}: ${err.message}`);
       return [];
     }
   }
   async getFileChurn(filePath) {
     try {
-      const log = await this.git.log({ file: filePath, "--follow": null });
+      const log3 = await this.git.log({ file: filePath, "--follow": null });
       return {
         filePath,
-        commitCount: log.total
+        commitCount: log3.total
       };
     } catch (err) {
-      console.error(`[ctxo:git] Failed to get churn for ${filePath}: ${err.message}`);
+      log2.error(` Failed to get churn for ${filePath}: ${err.message}`);
       return { filePath, commitCount: 0 };
     }
   }
@@ -402,9 +479,83 @@ var RevertDetector = class {
   }
 };
 
+// src/core/co-change/co-change-analyzer.ts
+var MIN_SHARED_COMMITS = 2;
+var MIN_FREQUENCY = 0.1;
+function aggregateCoChanges(indices) {
+  const commitToFiles = /* @__PURE__ */ new Map();
+  const fileCommitCounts = /* @__PURE__ */ new Map();
+  for (const idx of indices) {
+    const file = idx.file;
+    let count = 0;
+    for (const intent of idx.intent) {
+      count++;
+      let files = commitToFiles.get(intent.hash);
+      if (!files) {
+        files = /* @__PURE__ */ new Set();
+        commitToFiles.set(intent.hash, files);
+      }
+      files.add(file);
+    }
+    if (count > 0) {
+      fileCommitCounts.set(file, count);
+    }
+  }
+  const pairCounts = /* @__PURE__ */ new Map();
+  for (const files of commitToFiles.values()) {
+    if (files.size < 2) continue;
+    const sorted = [...files].sort();
+    for (let i = 0; i < sorted.length; i++) {
+      for (let j = i + 1; j < sorted.length; j++) {
+        const key = `${sorted[i]}|${sorted[j]}`;
+        pairCounts.set(key, (pairCounts.get(key) ?? 0) + 1);
+      }
+    }
+  }
+  const entries = [];
+  for (const [key, sharedCommits] of pairCounts) {
+    if (sharedCommits < MIN_SHARED_COMMITS) continue;
+    const [file1, file2] = key.split("|");
+    const count1 = fileCommitCounts.get(file1) ?? 0;
+    const count2 = fileCommitCounts.get(file2) ?? 0;
+    const minCount = Math.min(count1, count2);
+    if (minCount === 0) continue;
+    const frequency = Math.round(sharedCommits / minCount * 1e3) / 1e3;
+    if (frequency < MIN_FREQUENCY) continue;
+    entries.push({ file1, file2, sharedCommits, frequency });
+  }
+  entries.sort((a, b) => b.frequency - a.frequency || b.sharedCommits - a.sharedCommits);
+  return {
+    version: 1,
+    timestamp: Math.floor(Date.now() / 1e3),
+    entries
+  };
+}
+function loadCoChangeMap(matrix) {
+  const map = /* @__PURE__ */ new Map();
+  for (const entry of matrix.entries) {
+    let list1 = map.get(entry.file1);
+    if (!list1) {
+      list1 = [];
+      map.set(entry.file1, list1);
+    }
+    list1.push(entry);
+    let list2 = map.get(entry.file2);
+    if (!list2) {
+      list2 = [];
+      map.set(entry.file2, list2);
+    }
+    list2.push(entry);
+  }
+  return map;
+}
+
 export {
+  createLogger,
   SqliteStorageAdapter,
   RevertDetector,
-  SimpleGitAdapter
+  SimpleGitAdapter,
+  aggregateCoChanges,
+  loadCoChangeMap
 };
-//# sourceMappingURL=chunk-P7JUSY3I.js.map
+//# sourceMappingURL=chunk-XSHNN6PU.js.map

package/dist/chunk-XSHNN6PU.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/core/why-context/revert-detector.ts","../src/core/co-change/co-change-analyzer.ts"],"sourcesContent":["/**\n * Structured logger for Ctxo — all output goes to stderr (stdout reserved for MCP JSON-RPC).\n *\n * Supports debug mode via DEBUG environment variable:\n *   DEBUG=ctxo:*          — all debug output\n *   DEBUG=ctxo:git        — only git adapter debug\n *   DEBUG=ctxo:index      — only indexing debug\n *   DEBUG=ctxo:mcp        — only MCP handler debug\n *   DEBUG=ctxo:storage    — only storage adapter debug\n *   DEBUG=ctxo:masking    — only masking pipeline debug\n *\n * Always outputs: info, warn, error (regardless of DEBUG).\n * Only outputs debug when matching namespace is enabled.\n */\n\nfunction isDebugEnabled(namespace: string): boolean {\n  const debugEnv = process.env['DEBUG'] ?? '';\n  if (!debugEnv) return false;\n  const patterns = debugEnv.split(',').map(p => p.trim());\n  return patterns.some(p => {\n    if (p === '*' || p === 'ctxo:*') return true;\n    if (p === namespace) return true;\n    if (p.endsWith(':*') && namespace.startsWith(p.slice(0, -1))) return true;\n    return false;\n  });\n}\n\nexport interface Logger {\n  debug(message: string, ...args: unknown[]): void;\n  info(message: string, ...args: unknown[]): void;\n  warn(message: string, ...args: unknown[]): void;\n  error(message: string, ...args: unknown[]): void;\n}\n\nexport function createLogger(namespace: string): Logger {\n  const prefix = `[${namespace}]`;\n\n  return {\n    debug(message: string, ...args: unknown[]) {\n      if (isDebugEnabled(namespace)) {\n        console.error(`${prefix} DEBUG ${message}`, ...args);\n      }\n    },\n    info(message: string, ...args: unknown[]) {\n      console.error(`${prefix} ${message}`, ...args);\n    },\n    warn(message: string, ...args: unknown[]) {\n      console.error(`${prefix} WARN ${message}`, ...args);\n    },\n    error(message: string, ...args: unknown[]) {\n      console.error(`${prefix} ERROR ${message}`, ...args);\n    },\n  };\n}\n","import initSqlJs, { type Database } from 'sql.js';\nimport { readFileSync, writeFileSync, existsSync, mkdirSync } from 'node:fs';\nimport { join, dirname } from 'node:path';\nimport type { FileIndex, GraphEdge, SymbolNode } from '../../core/types.js';\nimport type { IStoragePort } from '../../ports/i-storage-port.js';\nimport { JsonIndexReader } from './json-index-reader.js';\nimport { createLogger } from '../../core/logger.js';\n\nconst log = createLogger('ctxo:storage');\n\nexport class SqliteStorageAdapter implements IStoragePort {\n  private db: Database | undefined;\n  private readonly dbPath: string;\n  private readonly ctxoRoot: string;\n\n  constructor(ctxoRoot: string) {\n    this.ctxoRoot = ctxoRoot;\n    this.dbPath = join(ctxoRoot, '.cache', 'symbols.db');\n  }\n\n  async init(): Promise<void> {\n    const SQL = await initSqlJs();\n\n    if (existsSync(this.dbPath)) {\n      try {\n        const buffer = readFileSync(this.dbPath);\n        this.db = new SQL.Database(buffer);\n        this.verifyIntegrity();\n      } catch {\n        log.warn('Corrupt DB detected, rebuilding from JSON index');\n        this.db = new SQL.Database();\n        this.createTables();\n      }\n    } else {\n      this.db = new SQL.Database();\n      this.createTables();\n    }\n\n    // Always rebuild from JSON — it is the source of truth\n    this.rebuildFromJson();\n  }\n\n  async initEmpty(): Promise<void> {\n    const SQL = await initSqlJs();\n    this.db = new SQL.Database();\n    this.createTables();\n  }\n\n  private database(): Database {\n    if (!this.db) {\n      throw new Error('SqliteStorageAdapter not initialized. Call init() first.');\n    }\n    return this.db;\n  }\n\n  private verifyIntegrity(): void {\n    const db = this.database();\n    const result = db.exec('PRAGMA integrity_check');\n    const firstRow = result[0]?.values[0];\n    if (!firstRow || firstRow[0] !== 'ok') {\n      throw new Error('SQLite integrity check failed');\n    }\n\n    const tables = db.exec(\n      \"SELECT name FROM sqlite_master WHERE type='table' AND name IN ('symbols', 'edges', 'files')\",\n    );\n    if (!tables[0] || tables[0].values.length < 3) {\n      throw new Error('Missing required tables');\n    }\n  }\n\n  private createTables(): void {\n    const db = this.database();\n    db.run(`\n      CREATE TABLE IF NOT EXISTS files (\n        file_path TEXT PRIMARY KEY,\n        last_modified INTEGER NOT NULL\n      )\n    `);\n    db.run(`\n      CREATE TABLE IF NOT EXISTS symbols (\n        symbol_id TEXT PRIMARY KEY,\n        name TEXT NOT NULL,\n        kind TEXT NOT NULL,\n        file_path TEXT NOT NULL,\n        start_line INTEGER NOT NULL,\n        end_line INTEGER NOT NULL\n      )\n    `);\n    db.run(`\n      CREATE TABLE IF NOT EXISTS edges (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        from_symbol TEXT NOT NULL,\n        to_symbol TEXT NOT NULL,\n        kind TEXT NOT NULL\n      )\n    `);\n    db.run('CREATE INDEX IF NOT EXISTS idx_symbols_file ON symbols(file_path)');\n    db.run('CREATE INDEX IF NOT EXISTS idx_edges_from ON edges(from_symbol)');\n    db.run('CREATE INDEX IF NOT EXISTS idx_edges_to ON edges(to_symbol)');\n  }\n\n  private rebuildFromJson(): void {\n    const reader = new JsonIndexReader(this.ctxoRoot);\n    const indices = reader.readAll();\n\n    if (indices.length > 0) {\n      this.bulkWrite(indices);\n    }\n  }\n\n  writeSymbolFile(fileIndex: FileIndex): void {\n    const db = this.database();\n\n    db.run('BEGIN TRANSACTION');\n    try {\n      this.deleteFileData(db, fileIndex.file);\n\n      db.run(\n        'INSERT INTO files (file_path, last_modified) VALUES (?, ?)',\n        [fileIndex.file, fileIndex.lastModified],\n      );\n\n      for (const sym of fileIndex.symbols) {\n        db.run(\n          'INSERT OR REPLACE INTO symbols (symbol_id, name, kind, file_path, start_line, end_line) VALUES (?, ?, ?, ?, ?, ?)',\n          [sym.symbolId, sym.name, sym.kind, fileIndex.file, sym.startLine, sym.endLine],\n        );\n      }\n\n      for (const edge of fileIndex.edges) {\n        db.run(\n          'INSERT INTO edges (from_symbol, to_symbol, kind) VALUES (?, ?, ?)',\n          [edge.from, edge.to, edge.kind],\n        );\n      }\n\n      db.run('COMMIT');\n      this.persistIfNeeded();\n    } catch (err) {\n      db.run('ROLLBACK');\n      throw err;\n    }\n  }\n\n  /**\n   * Read symbol file from SQLite cache.\n   * NOTE: SQLite only caches symbols + edges (graph topology).\n   * intent, antiPatterns, and complexity live in committed JSON index only.\n   * Use JsonIndexReader for full FileIndex data.\n   */\n  readSymbolFile(relativePath: string): FileIndex | undefined {\n    const db = this.database();\n\n    const fileResult = db.exec(\n      'SELECT file_path, last_modified FROM files WHERE file_path = ?',\n      [relativePath],\n    );\n    if (!fileResult[0] || fileResult[0].values.length === 0) {\n      return undefined;\n    }\n\n    const [filePath, lastModified] = fileResult[0].values[0] as [string, number];\n\n    const symbols = this.getSymbolsForFile(db, filePath);\n    const edges = this.getEdgesForFile(db, filePath);\n\n    return {\n      file: filePath,\n      lastModified,\n      symbols,\n      edges,\n      // Not stored in SQLite — use JsonIndexReader for these fields\n      intent: [],\n      antiPatterns: [],\n    };\n  }\n\n  listIndexedFiles(): string[] {\n    const db = this.database();\n    const result = db.exec('SELECT file_path FROM files ORDER BY file_path');\n    if (!result[0]) return [];\n    return result[0].values.map((row) => row[0] as string);\n  }\n\n  deleteSymbolFile(relativePath: string): void {\n    const db = this.database();\n    this.deleteFileData(db, relativePath);\n  }\n\n  getSymbolById(symbolId: string): SymbolNode | undefined {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT symbol_id, name, kind, start_line, end_line FROM symbols WHERE symbol_id = ?',\n      [symbolId],\n    );\n    if (!result[0] || result[0].values.length === 0) {\n      return undefined;\n    }\n\n    const [sid, name, kind, startLine, endLine] = result[0].values[0] as [string, string, string, number, number];\n    return { symbolId: sid, name, kind: kind as SymbolNode['kind'], startLine, endLine };\n  }\n\n  getEdgesFrom(symbolId: string): GraphEdge[] {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT from_symbol, to_symbol, kind FROM edges WHERE from_symbol = ?',\n      [symbolId],\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      from: row[0] as string,\n      to: row[1] as string,\n      kind: row[2] as GraphEdge['kind'],\n    }));\n  }\n\n  getEdgesTo(symbolId: string): GraphEdge[] {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT from_symbol, to_symbol, kind FROM edges WHERE to_symbol = ?',\n      [symbolId],\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      from: row[0] as string,\n      to: row[1] as string,\n      kind: row[2] as GraphEdge['kind'],\n    }));\n  }\n\n  getAllSymbols(): SymbolNode[] {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT symbol_id, name, kind, start_line, end_line FROM symbols',\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      symbolId: row[0] as string,\n      name: row[1] as string,\n      kind: row[2] as SymbolNode['kind'],\n      startLine: row[3] as number,\n      endLine: row[4] as number,\n    }));\n  }\n\n  getAllEdges(): GraphEdge[] {\n    const db = this.database();\n    const result = db.exec(\n      'SELECT from_symbol, to_symbol, kind FROM edges',\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      from: row[0] as string,\n      to: row[1] as string,\n      kind: row[2] as GraphEdge['kind'],\n    }));\n  }\n\n  bulkWrite(indices: FileIndex[]): void {\n    const db = this.database();\n\n    db.run('BEGIN TRANSACTION');\n    try {\n      for (const fileIndex of indices) {\n        this.deleteFileData(db, fileIndex.file);\n\n        db.run(\n          'INSERT INTO files (file_path, last_modified) VALUES (?, ?)',\n          [fileIndex.file, fileIndex.lastModified],\n        );\n\n        for (const sym of fileIndex.symbols) {\n          db.run(\n            'INSERT OR REPLACE INTO symbols (symbol_id, name, kind, file_path, start_line, end_line) VALUES (?, ?, ?, ?, ?, ?)',\n            [sym.symbolId, sym.name, sym.kind, fileIndex.file, sym.startLine, sym.endLine],\n          );\n        }\n\n        for (const edge of fileIndex.edges) {\n          db.run(\n            'INSERT INTO edges (from_symbol, to_symbol, kind) VALUES (?, ?, ?)',\n            [edge.from, edge.to, edge.kind],\n          );\n        }\n      }\n\n      db.run('COMMIT');\n      this.persistIfNeeded();\n    } catch (err) {\n      db.run('ROLLBACK');\n      throw err;\n    }\n  }\n\n  persist(): void {\n    const db = this.database();\n    const data = db.export();\n    const buffer = Buffer.from(data);\n    mkdirSync(dirname(this.dbPath), { recursive: true });\n    writeFileSync(this.dbPath, buffer);\n  }\n\n  close(): void {\n    if (this.db) {\n      this.persist();\n      this.db.close();\n      this.db = undefined;\n    }\n  }\n\n  private persistIfNeeded(): void {\n    try {\n      this.persist();\n    } catch (err) {\n      log.error(`Failed to persist DB: ${(err as Error).message}`);\n    }\n  }\n\n  private deleteFileData(db: Database, filePath: string): void {\n    // Delete edges originating from this file's symbols\n    const symResult = db.exec(\n      'SELECT symbol_id FROM symbols WHERE file_path = ?',\n      [filePath],\n    );\n    if (symResult[0]) {\n      for (const row of symResult[0].values) {\n        db.run('DELETE FROM edges WHERE from_symbol = ?', [row[0]]);\n      }\n    }\n    db.run('DELETE FROM symbols WHERE file_path = ?', [filePath]);\n    db.run('DELETE FROM files WHERE file_path = ?', [filePath]);\n  }\n\n  private getSymbolsForFile(db: Database, filePath: string): SymbolNode[] {\n    const result = db.exec(\n      'SELECT symbol_id, name, kind, start_line, end_line FROM symbols WHERE file_path = ? ORDER BY start_line',\n      [filePath],\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      symbolId: row[0] as string,\n      name: row[1] as string,\n      kind: row[2] as SymbolNode['kind'],\n      startLine: row[3] as number,\n      endLine: row[4] as number,\n    }));\n  }\n\n  private getEdgesForFile(db: Database, filePath: string): GraphEdge[] {\n    const result = db.exec(\n      `SELECT e.from_symbol, e.to_symbol, e.kind FROM edges e\n       INNER JOIN symbols s ON e.from_symbol = s.symbol_id\n       WHERE s.file_path = ?`,\n      [filePath],\n    );\n    if (!result[0]) return [];\n    return result[0].values.map((row) => ({\n      from: row[0] as string,\n      to: row[1] as string,\n      kind: row[2] as GraphEdge['kind'],\n    }));\n  }\n}\n","import { simpleGit, type SimpleGit } from 'simple-git';\nimport type { IGitPort } from '../../ports/i-git-port.js';\nimport type { CommitRecord, ChurnData } from '../../core/types.js';\nimport { createLogger } from '../../core/logger.js';\n\nconst log = createLogger('ctxo:git');\n\nexport class SimpleGitAdapter implements IGitPort {\n  private readonly git: SimpleGit;\n\n  constructor(projectRoot: string) {\n    this.git = simpleGit(projectRoot);\n    log.debug('Initialized with root: %s', projectRoot);\n  }\n\n  async isAvailable(): Promise<boolean> {\n    try {\n      await this.git.version();\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  async getCommitHistory(filePath: string, maxCount?: number): Promise<CommitRecord[]> {\n    try {\n      const log = await this.git.log({\n        file: filePath,\n        '--follow': null,\n        ...(maxCount ? { maxCount } : {}),\n      });\n\n      return log.all.map((entry) => ({\n        hash: entry.hash,\n        message: entry.message,\n        date: entry.date,\n        author: entry.author_name,\n      }));\n    } catch (err) {\n      log.error(` Failed to get history for ${filePath}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  async getBatchHistory(maxCount = 20): Promise<Map<string, CommitRecord[]>> {\n    try {\n      const log = await this.git.log({ maxCount: maxCount * 50, '--name-only': null });\n      const result = new Map<string, CommitRecord[]>();\n\n      for (const entry of log.all) {\n        const record: CommitRecord = {\n          hash: entry.hash,\n          message: entry.message,\n          date: entry.date,\n          author: entry.author_name,\n        };\n\n        const diff = entry.diff;\n        const files: string[] = diff?.files?.map((f: { file: string }) => f.file.replace(/\\\\/g, '/')) ?? [];\n\n        for (const file of files) {\n          let list = result.get(file);\n          if (!list) { list = []; result.set(file, list); }\n          if (list.length < maxCount) {\n            list.push(record);\n          }\n        }\n      }\n\n      return result;\n    } catch (err) {\n      log.error(` Batch history failed: ${(err as Error).message}`);\n      return new Map();\n    }\n  }\n\n  async getChangedFiles(since: string): Promise<string[]> {\n    try {\n      const diff = await this.git.diffSummary([since]);\n      return diff.files.map((f) => f.file.replace(/\\\\/g, '/'));\n    } catch (err) {\n      log.error(` Failed to get changed files since ${since}: ${(err as Error).message}`);\n      return [];\n    }\n  }\n\n  async getFileChurn(filePath: string): Promise<ChurnData> {\n    try {\n      const log = await this.git.log({ file: filePath, '--follow': null });\n\n      return {\n        filePath,\n        commitCount: log.total,\n      };\n    } catch (err) {\n      log.error(` Failed to get churn for ${filePath}: ${(err as Error).message}`);\n      return { filePath, commitCount: 0 };\n    }\n  }\n}\n","import type { CommitRecord, AntiPattern } from '../types.js';\n\n// Explicit revert patterns\nconst REVERT_QUOTED_PATTERN = /^Revert \"(.+)\"$/;\nconst REVERT_PREFIX_PATTERN = /^revert:\\s*(.+)$/i;\n\n// Undo/rollback patterns\nconst UNDO_PATTERN = /^undo[:\\s]/i;\nconst ROLLBACK_PATTERN = /^rollback[:\\s]/i;\n\n// Indirect revert indicators (keywords in commit message body)\nconst INDIRECT_KEYWORDS = [\n  /\\brevert(?:s|ed|ing)?\\b/i,\n  /\\broll(?:s|ed|ing)?\\s*back\\b/i,\n  /\\bundo(?:es|ne|ing)?\\b/i,\n  /\\bbacked?\\s*out\\b/i,\n  /\\bremov(?:e|es|ed|ing)\\s+(?:broken|buggy|faulty)\\b/i,\n];\n\nexport class RevertDetector {\n  detect(commits: readonly CommitRecord[]): AntiPattern[] {\n    const antiPatterns: AntiPattern[] = [];\n\n    for (const commit of commits) {\n      if (!commit.message) continue;\n\n      if (this.isRevert(commit.message)) {\n        antiPatterns.push({\n          hash: commit.hash,\n          message: commit.message,\n          date: commit.date,\n        });\n      }\n    }\n\n    return antiPatterns;\n  }\n\n  private isRevert(message: string): boolean {\n    // Explicit patterns (high confidence)\n    if (REVERT_QUOTED_PATTERN.test(message)) return true;\n    if (REVERT_PREFIX_PATTERN.test(message)) return true;\n    if (UNDO_PATTERN.test(message)) return true;\n    if (ROLLBACK_PATTERN.test(message)) return true;\n\n    // Indirect indicators (keyword search in full message)\n    for (const pattern of INDIRECT_KEYWORDS) {\n      if (pattern.test(message)) return true;\n    }\n\n    return false;\n  }\n}\n","import type { CoChangeEntry, CoChangeMatrix, FileIndex } from '../types.js';\n\nconst MIN_SHARED_COMMITS = 2;\nconst MIN_FREQUENCY = 0.1;\n\nexport function aggregateCoChanges(indices: readonly FileIndex[]): CoChangeMatrix {\n  // Step 1: Build commit → files map\n  const commitToFiles = new Map<string, Set<string>>();\n  const fileCommitCounts = new Map<string, number>();\n\n  for (const idx of indices) {\n    const file = idx.file;\n    let count = 0;\n    for (const intent of idx.intent) {\n      count++;\n      let files = commitToFiles.get(intent.hash);\n      if (!files) {\n        files = new Set();\n        commitToFiles.set(intent.hash, files);\n      }\n      files.add(file);\n    }\n    if (count > 0) {\n      fileCommitCounts.set(file, count);\n    }\n  }\n\n  // Step 2: Count shared commits per file pair\n  const pairCounts = new Map<string, number>();\n  for (const files of commitToFiles.values()) {\n    if (files.size < 2) continue;\n    const sorted = [...files].sort();\n    for (let i = 0; i < sorted.length; i++) {\n      for (let j = i + 1; j < sorted.length; j++) {\n        const key = `${sorted[i]}|${sorted[j]}`;\n        pairCounts.set(key, (pairCounts.get(key) ?? 0) + 1);\n      }\n    }\n  }\n\n  // Step 3: Calculate frequency and filter\n  const entries: CoChangeEntry[] = [];\n  for (const [key, sharedCommits] of pairCounts) {\n    if (sharedCommits < MIN_SHARED_COMMITS) continue;\n\n    const [file1, file2] = key.split('|') as [string, string];\n    const count1 = fileCommitCounts.get(file1) ?? 0;\n    const count2 = fileCommitCounts.get(file2) ?? 0;\n    const minCount = Math.min(count1, count2);\n    if (minCount === 0) continue;\n\n    const frequency = Math.round((sharedCommits / minCount) * 1000) / 1000;\n    if (frequency < MIN_FREQUENCY) continue;\n\n    entries.push({ file1, file2, sharedCommits, frequency });\n  }\n\n  entries.sort((a, b) => b.frequency - a.frequency || b.sharedCommits - a.sharedCommits);\n\n  return {\n    version: 1,\n    timestamp: Math.floor(Date.now() / 1000),\n    entries,\n  };\n}\n\nexport function loadCoChangeMap(matrix: CoChangeMatrix): Map<string, CoChangeEntry[]> {\n  const map = new Map<string, CoChangeEntry[]>();\n  for (const entry of matrix.entries) {\n    let list1 = map.get(entry.file1);\n    if (!list1) { list1 = []; map.set(entry.file1, list1); }\n    list1.push(entry);\n\n    let list2 = map.get(entry.file2);\n    if (!list2) { list2 = []; map.set(entry.file2, list2); }\n    list2.push(entry);\n  }\n  return 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