@vohongtho.infotech/code-intel 1.0.2 → 1.0.3

package/README.md

@@ -1,6 +1,6 @@
 # Code Intelligence Platform
 
-[![npm version](https://img.shields.io/badge/npm-v1.0.1-blue)](https://www.npmjs.com/package/@vohongtho.infotech/code-intel)
+[![npm version](https://img.shields.io/badge/npm-v1.0.3-blue)](https://www.npmjs.com/package/@vohongtho.infotech/code-intel)
 
 A static code analysis platform that builds a **Knowledge Graph** from your source code and makes it explorable through a Web UI, HTTP API, CLI, and MCP server.
 
@@ -31,7 +31,7 @@ A static code analysis platform that builds a **Knowledge Graph** from your sour
 - **Multi-language** — TypeScript, JavaScript, Python, Java, Go, C, C++, C#, Rust, PHP, Ruby, Swift, Kotlin, Dart (14 languages via tree-sitter AST)
 - **Incremental Analysis** — `--incremental` flag re-parses only git-changed/mtime-changed files; 10k-file repo with 3 changes: 288ms
 - **Parallel Analysis** — `--parallel` flag runs parse + resolve phases on worker threads for large repos
-- **AI Context Files** — auto-generates `AGENTS.md`, `CLAUDE.md`, `.github/copilot-instructions.md`, `.cursor/rules/code-intel.mdc`, `.kiro/steering/code-intel.md`, `.clinerules`, `.windsurfrules`, `.kilocode/rules/code-intel-rules.md`, and `.agents/rules/code-intel-rules.md` after every analysis — supporting Amp, Claude Code, Codex, Copilot, Cursor, Aider, Gemini, Kiro, Trae, Hermes, Factory, OpenCode, Pi, Antigravity, OpenClaw, Cline, Windsurf, Kilo Code, and more
+- **AI Context Files** — auto-generates `AGENTS.md` and `CLAUDE.md` after every analysis (universal, always written); agent-specific files (`.github/copilot-instructions.md`, `.cursor/rules/code-intel.mdc`, `.windsurfrules`) are written **only when the corresponding binary is detected on PATH** — never pollutes projects with files for tools the user doesn't have; `code-intel setup` writes all files for user-initiated one-time setup — supporting Amp, Claude Code, Codex, Copilot, Cursor, Aider, Gemini, Kiro, OpenCode, Trae, Hermes, Factory, Pi, Antigravity, OpenClaw, Cline, Windsurf, Kilo Code, and more
 - **Agent Hook System** _(v1.0.2)_ — `code-intel setup` installs PreToolUse hooks for all major AI agents; when an agent runs `grep MyClass src/`, the `code-intel-hook` binary (~10KB, ~50ms startup) silently rewrites it to `code-intel search "MyClass"` — saving ~3,000 tokens per lookup; supports Claude Code, Cursor, Gemini CLI, GitHub Copilot (VS Code + CLI), OpenCode, OpenClaw; rules files for Cline/Roo Code, Windsurf, Kilo Code, Antigravity, Codex CLI
 - **Skill Files** — generates `.claude/skills/code-intel/` with per-cluster SKILL.md files (hot symbols, entry points, impact guidance) for AI assistants
 - **Repository Groups** — multi-repo / monorepo service tracking with workspace auto-discovery (npm, pnpm, Nx, Turborepo), contract extraction (OpenAPI, GraphQL, Protobuf), type-aware similarity scoring, and cross-repo dependency detection
@@ -55,6 +55,15 @@ A static code analysis platform that builds a **Knowledge Graph** from your sour
 - **Token-Efficient MCP** _(v1.0.1)_ — compact JSON responses (null/undefined stripped); MCP tool defaults tuned for LLM sessions: `search`/`file_symbols`/`list_exports` default 10 results (was 50), `blast_radius`/`pr_impact` default 2 hops (was 5); `suggested_next_tools` opt-in via `CODE_INTEL_SUGGEST_NEXT_TOOLS=true`; ~63% fewer tokens per typical 5-tool session
 - **Context Builder** _(v1.0.1)_ — `src/context/builder.ts` builds structured `[SUMMARY]` / `[LOGIC]` / `[RELATION]` / `[FOCUS CODE]` documents from seed symbols in ≤50% of v1.0.0 token cost; query-intent presets (`code`, `callers`, `architecture`, `auto`); adaptive snippets; cross-block dedup; `code-intel context <symbols...> --show-context`
 - **Enforced Tool Policy in AI Context Files** _(v1.0.1)_ — `AGENTS.md`/`CLAUDE.md`/`copilot-instructions.md`/`.cursor/rules`/`.kiro/steering` now include a `TOOL POLICY: ENFORCED` block forbidding raw `grep`/`find`/`cat` in favour of `code-intel search` → `inspect` → `impact`; saves ~3,000 tokens per cold-file lookup
+- **Inspect Disambiguation** _(v1.0.3)_ — `inspect` now detects when a symbol name exists in multiple files; CLI shows a multi-match warning listing all candidates with source previews and suggests `--file`; MCP returns a `disambiguation` JSON object instead of silently resolving the wrong class
+- **`--file` flag for CLI** _(v1.0.3)_ — `inspect <symbol> --file <pattern>` and `impact <symbol> --file <pattern>` select the correct implementation when the same name exists across multiple modules (e.g. `login` in API vs CMS, `requestAccessToken` in JWT vs Token)
+- **`code-intel read <file>`** _(v1.0.3)_ — new CLI command reads raw source lines from any indexed file using partial path matching; supports `--start`/`--end` line range (max 300 lines per call); essential for reading config files with no indexable symbols
+- **MCP `get_source` tool** _(v1.0.3)_ — MCP equivalent of `read`; reads raw numbered source lines from any indexed file by partial path; accepts `start_line`/`end_line`; returns `hasMore` flag for pagination
+- **BM25 Class-Name Boosting** _(v1.0.3)_ — file basename (class name) now weighted strongly in BM25 documents; queries like `"Token requestAccessToken"` rank the Token class above JWT for same-named methods; content window expanded 1 000 → 1 500 chars
+- **Claude Code Plugin — PostToolUse & Augment** _(v1.0.3)_ — `code-intel hook claude` now handles both `PreToolUse` (command rewrite + graph context injection) and `PostToolUse` (stale-index notification after git commit/merge/pull via HEAD vs `.code-intel/meta.json` comparison); new `code-intel augment -- <pattern>` command injects compact symbol context (`in:N out:N` call counts, snippet) into the agent before grep/rg/cat calls; `code-intel hook <agent>` now supports `claude | cursor | gemini | copilot`
+- **`analyze` no longer creates unwanted agent files** _(v1.0.3-patch)_ — strict binary-only gate: no binary = no file, period; pre-existing files from old runs are NOT updated unless the binary is present; `AGENTS.md` and `CLAUDE.md` always written; Kiro, Cline, Kilo Code, Antigravity files are setup-only and never touched by `analyze`
+- **Cross-OS Agent Detection & MCP Registration** _(v1.0.3)_ — `init` and `setup` agent detection and MCP config writing now work correctly on Ubuntu, macOS, and Windows; `commandExists()` uses `execFileSync('which'/'where')` instead of a broken shell-composed string; OS-aware path helpers resolve the right config directories; atomic rename retries up to 5× on Windows transient file-lock errors; `npx`-based MCP entry used for all agents
+- **Safe MCP config merging — zero data loss** _(v1.0.3-patch)_ — `mergeJsonFile()` creates a `.bak` backup before every write; Amp uses root-level flat-key merge so no `"amp.*"` settings are destroyed; all agents check idempotency before writing; Kiro IDE and OpenCode added as first-class `setup` agents with correct config formats
 
 ---
 

package/dist/cli/hook.js

@@ -1,6 +1,86 @@
 #!/usr/bin/env node
 import process2 from 'process';
+import fs from 'fs';
+import path from 'path';
+import { spawnSync } from 'child_process';
 
+function findCodeIntelDir(startDir) {
+  let dir = startDir;
+  for (let i = 0; i < 8; i++) {
+    const candidate = path.join(dir, ".code-intel");
+    try {
+      if (fs.statSync(candidate).isDirectory()) return candidate;
+    } catch {
+    }
+    const parent = path.dirname(dir);
+    if (parent === dir) break;
+    dir = parent;
+  }
+  return null;
+}
+function loadIndexedCommit(codeIntelDir) {
+  try {
+    const meta = JSON.parse(fs.readFileSync(path.join(codeIntelDir, "meta.json"), "utf-8"));
+    return meta.commitHash ?? "";
+  } catch {
+    return "";
+  }
+}
+function getHeadCommit(cwd) {
+  try {
+    const r = spawnSync("git", ["rev-parse", "HEAD"], {
+      encoding: "utf-8",
+      timeout: 3e3,
+      cwd,
+      stdio: ["pipe", "pipe", "pipe"]
+    });
+    return (r.stdout ?? "").trim();
+  } catch {
+    return "";
+  }
+}
+function runCodeIntelAugment(pattern, cwd) {
+  const isWin = process2.platform === "win32";
+  const bin = isWin ? "code-intel.cmd" : "code-intel";
+  const npxBin = isWin ? "npx.cmd" : "npx";
+  let r = spawnSync(bin, ["augment", "--", pattern], {
+    encoding: "utf-8",
+    timeout: 6e3,
+    cwd,
+    stdio: ["pipe", "pipe", "pipe"]
+  });
+  if (r.error || r.status !== 0) {
+    r = spawnSync(npxBin, ["code-intel", "augment", "--", pattern], {
+      encoding: "utf-8",
+      timeout: 1e4,
+      cwd,
+      stdio: ["pipe", "pipe", "pipe"]
+    });
+  }
+  return !r.error && r.status === 0 ? (r.stdout ?? "").trim() : "";
+}
+function handlePostToolUse(input) {
+  const toolName = input.tool_name ?? "";
+  if (toolName !== "Bash") return;
+  const command = input.tool_input?.command ?? "";
+  if (!/\bgit\s+(commit|merge|rebase|cherry-pick|pull)(\s|$)/.test(command)) return;
+  const exitCode = input.tool_output?.exit_code;
+  if (exitCode !== void 0 && exitCode !== 0) return;
+  const cwd = input.cwd ?? process2.cwd();
+  if (!path.isAbsolute(cwd)) return;
+  const codeIntelDir = findCodeIntelDir(cwd);
+  if (!codeIntelDir) return;
+  const head = getHeadCommit(cwd);
+  if (!head) return;
+  const indexed = loadIndexedCommit(codeIntelDir);
+  if (head && head === indexed) return;
+  const since = indexed ? indexed.slice(0, 7) : "never";
+  const current = head.slice(0, 7);
+  const msg = `code-intel index is stale (last indexed: ${since}, current HEAD: ${current}). Run \`code-intel analyze\` to update the knowledge graph.`;
+  process2.stdout.write(
+    JSON.stringify({ hookSpecificOutput: { hookEventName: "PostToolUse", additionalContext: msg } })
+  );
+}
 var SOURCE_EXT = /* @__PURE__ */ new Set([
   "ts",
   "tsx",
@@ -289,26 +369,49 @@ function runClaudeHook() {
         process2.exit(0);
       }
       const parsed = JSON.parse(input);
-      const cmd = parsed?.tool_input?.command;
-      if (typeof cmd !== "string" || !cmd.trim()) {
+      const hookEvent = parsed.hook_event_name ?? "PreToolUse";
+      if (hookEvent === "PostToolUse") {
+        handlePostToolUse(parsed);
         process2.exit(0);
       }
-      const rewritten = rewriteCommand(cmd);
-      if (rewritten === null || rewritten === cmd) {
+      const toolInput = parsed.tool_input;
+      const cmd = toolInput?.command;
+      if (typeof cmd !== "string" || !cmd.trim()) {
         process2.exit(0);
       }
-      const response = {
-        hookSpecificOutput: {
-          hookEventName: "PreToolUse",
-          permissionDecision: "allow",
-          permissionDecisionReason: "code-intel: semantic search replaces grep/cat",
-          updatedInput: {
-            ...parsed.tool_input,
-            command: rewritten
+      const rewritten = rewriteCommand(cmd);
+      const cwd = parsed.cwd ?? process2.cwd();
+      let additionalContext;
+      try {
+        if (path.isAbsolute(cwd) && findCodeIntelDir(cwd)) {
+          const pattern = extractGrepSymbol(cmd) ?? (rewritten ? void 0 : void 0);
+          if (pattern) {
+            const ctx = runCodeIntelAugment(pattern, cwd);
+            if (ctx) additionalContext = ctx;
           }
         }
-      };
-      process2.stdout.write(JSON.stringify(response));
+      } catch {
+      }
+      if (rewritten !== null && rewritten !== cmd) {
+        const response = {
+          hookSpecificOutput: {
+            hookEventName: "PreToolUse",
+            permissionDecision: "allow",
+            permissionDecisionReason: "code-intel: semantic search replaces grep/cat",
+            updatedInput: { ...toolInput, command: rewritten },
+            ...additionalContext ? { additionalContext } : {}
+          }
+        };
+        process2.stdout.write(JSON.stringify(response));
+      } else if (additionalContext) {
+        const response = {
+          hookSpecificOutput: {
+            hookEventName: "PreToolUse",
+            additionalContext
+          }
+        };
+        process2.stdout.write(JSON.stringify(response));
+      }
       process2.exit(0);
     } catch {
       process2.exit(0);

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* hook-rewriter.ts\n *\n * Single source of truth for all command rewrite rules.\n * Equivalent to RTK's src/discover/rules.rs + src/discover/registry.rs.\n *\n * Called by:\n *   - `code-intel rewrite <cmd>` → exit 0 (match) | exit 1 (no match)\n *   - `code-intel hook claude`   → reads stdin PreToolUse JSON, writes response JSON\n *\n * ZERO heavy imports — this module must load in <50ms.\n * No DB, no graph, no pipeline, no config, no filesystem access.\n */\n\nimport process from 'node:process';\n\n// ─── Source file extensions ───────────────────────────────────────────────────\n// Only these are worth inspecting via code-intel inspect.\n// All other file types (config, docs, logs, data) pass through unchanged.\n\nconst SOURCE_EXT = new Set([\n  'ts', 'tsx', 'js', 'jsx', 'mjs', 'cjs',\n  'py', 'pyi',\n  'rs',\n  'go',\n  'java', 'kt', 'kts',\n  'rb',\n  'cs',\n  'cpp', 'cc', 'cxx', 'c', 'h', 'hpp',\n  'swift',\n  'scala',\n  'php',\n]);\n\n// ─── Helpers ──────────────────────────────────────────────────────────────────\n\n/**\n * Regex metacharacters that indicate a true regex pattern, not a symbol name.\n * If a grep/rg search term contains any of these, we don't rewrite.\n */\nconst REGEX_META_RE = /[.*+?^${}()|[\\]\\\\]/;\n\n/**\n * A \"symbol-like\" identifier: starts with letter/$/_,\n * followed by alphanumeric/$/_/./- characters.\n * CamelCase, snake_case, dot.notation all qualify.\n */\nconst SYMBOL_ID_RE = /^[A-Za-z_$][A-Za-z0-9_$.-]*$/;\n\nfunction isSymbolLike(term: string): boolean {\n  return SYMBOL_ID_RE.test(term) && !REGEX_META_RE.test(term);\n}\n\nfunction isSourceFile(filePath: string): boolean {\n  const dot = filePath.lastIndexOf('.');\n  if (dot === -1) return false;\n  return SOURCE_EXT.has(filePath.slice(dot + 1).toLowerCase());\n}\n\n/** Extract the filename stem (basename without extension). */\nfunction fileStem(filePath: string): string {\n  const base = filePath.includes('/')\n    ? filePath.slice(filePath.lastIndexOf('/') + 1)\n    : filePath;\n  const dot = base.lastIndexOf('.');\n  return dot === -1 ? base : base.slice(0, dot);\n}\n\n/**\n * Extract a symbol-like search term from a grep or rg command.\n * Returns null if:\n *   - The term looks like a regex (contains metacharacters)\n *   - The flags indicate non-symbol-discovery use (-c, -v, -l, -L, -o, -Z)\n *   - No clear search term can be identified\n *\n * Flags that trigger passthrough (not symbol search):\n *   -c  count matches per file\n *   -v  invert match (select non-matching lines)\n *   -l  list files that have matches\n *   -L  list files that have NO matches\n *   -o  print only the matching part\n *   -Z  use NUL byte as line separator\n */\nfunction extractGrepSymbol(cmd: string): string | null {\n  // Reject if any flag group contains a non-symbol-discovery flag character.\n  // This regex looks for a dash followed by any combo of letters containing c/v/l/L/o/Z.\n  // We use a word-boundary aware pattern: -rnic is ok (r,n,i,I are fine),\n  // -rnc is not (c = count). The flag can appear anywhere after the command name.\n  if (/(?:^|\\s)-[a-zA-Z]*[cvlLoZ]/.test(cmd)) return null;\n\n  // Try double-quoted or single-quoted term first: grep \"Symbol\" or grep 'Symbol'\n  const quoted = cmd.match(/(?:^|\\s)[\"']([^\"']+)[\"'](?:\\s|$)/);\n  if (quoted) {\n    const term = quoted[1];\n    return isSymbolLike(term) ? term : null;\n  }\n\n  // Try unquoted term: skip command name and flags to find first bare identifier\n  const tokens = cmd.split(/\\s+/).slice(1); // skip 'grep' or 'rg'\n  for (const tok of tokens) {\n    if (tok.startsWith('-')) continue;                      // skip flags\n    if (tok.startsWith('/')) continue;                      // skip absolute paths\n    if (tok.startsWith('./') || tok.startsWith('../')) continue; // skip relative paths\n    if (tok.includes('/')) continue;                        // skip paths with slashes\n    if (tok === '.' || tok === '..') continue;              // skip dir shortcuts\n    // First non-flag, non-path token is the search pattern\n    return isSymbolLike(tok) ? tok : null;\n  }\n\n  return null;\n}\n\n// ─── Core rewrite function ────────────────────────────────────────────────────\n\n/**\n * Attempt to rewrite `cmd` to its code-intel equivalent.\n *\n * Returns the rewritten command string, or null if no rule matched.\n * NEVER throws — all rule errors silently degrade to null (passthrough).\n */\nexport function rewriteCommand(cmd: string): string | null {\n  try {\n    const trimmed = cmd.trim();\n    if (!trimmed) return null;\n\n    // ── Guard 1: Already a code-intel command (idempotency + anti-loop) ──────\n    // This prevents: code-intel search \"X\" → being rewritten again.\n    if (trimmed.startsWith('code-intel ') || trimmed === 'code-intel') return null;\n\n    // ── Guard 2: Compound commands — pass through in v1 ──────────────────────\n    // We don't attempt to split && || ; | in v1.\n    // A simple character scan is safe here since we check before any rule matching.\n    if (/(?:&&|\\|\\||;|\\|)/.test(trimmed)) return null;\n\n    // ── Rule 1: grep → code-intel search ─────────────────────────────────────\n    if (/^grep\\s/.test(trimmed)) {\n      const sym = extractGrepSymbol(trimmed);\n      if (sym) return `code-intel search \"${sym}\"`;\n      return null;\n    }\n\n    // ── Rule 2: rg → code-intel search ───────────────────────────────────────\n    if (/^rg\\s/.test(trimmed)) {\n      // Reject rg-specific structural flags (not symbol search)\n      if (/\\s--files(?:\\s|$)/.test(trimmed)) return null;\n      if (/\\s--files-with-matches(?:\\s|$)/.test(trimmed)) return null;\n      if (/\\s--type-not\\b/.test(trimmed)) return null;\n      const sym = extractGrepSymbol(trimmed);\n      if (sym) return `code-intel search \"${sym}\"`;\n      return null;\n    }\n\n    // ── Rule 3: cat <single-source-file> → code-intel inspect <stem> ─────────\n    if (/^cat\\s/.test(trimmed)) {\n      // Must be exactly: cat <one-token> — no multi-file, no options\n      const m = trimmed.match(/^cat\\s+(\\S+)$/);\n      if (!m) return null;           // multi-file or flags present\n      const filePath = m[1];\n      if (filePath === '-') return null;           // stdin passthrough\n      if (filePath.startsWith('>')) return null;   // write redirect\n      if (!isSourceFile(filePath)) return null;    // not a source file\n      return `code-intel inspect ${fileStem(filePath)}`;\n    }\n\n    // ── Rule 4: head/tail <single-source-file> → code-intel inspect <stem> ───\n    if (/^(?:head|tail)\\s/.test(trimmed)) {\n      if (/\\s-f\\b/.test(trimmed)) return null;     // tail -f = live follow, not inspection\n      // Accept common forms:\n      //   head <file>\n      //   head -N <file>\n      //   head -n N <file>\n      //   head --lines=N <file>\n      const m = trimmed.match(\n        /^(?:head|tail)\\s+(?:-\\d+\\s+|-n\\s+\\d+\\s+|--lines=\\d+\\s+)?(\\S+)$/,\n      );\n      if (!m) return null;\n      const filePath = m[1];\n      if (!isSourceFile(filePath)) return null;\n      return `code-intel inspect ${fileStem(filePath)}`;\n    }\n\n    return null;\n  } catch {\n    // Any unexpected error → silently pass through.\n    // A rule must NEVER cause the hook to crash.\n    return null;\n  }\n}\n\n// ─── CLI: `code-intel rewrite <cmd>` ─────────────────────────────────────────\n\n/**\n * Entry point for `code-intel rewrite <cmd>`.\n *\n * Exit codes (mirrors RTK exit code protocol):\n *   0 + stdout  → rewrite found; hook may auto-allow the rewritten command\n *   1           → no match; hook passes through unchanged\n */\nexport function runRewrite(cmd: string): never {\n  const rewritten = rewriteCommand(cmd.trim());\n  if (rewritten === null) {\n    process.exit(1);\n  }\n  process.stdout.write(rewritten);\n  process.exit(0);\n}\n\n// ─── CLI: `code-intel hook claude` ───────────────────────────────────────────\n\n/**\n * Entry point for `code-intel hook claude`.\n *\n * Reads a Claude Code PreToolUse JSON payload from stdin.\n * If the command matches a rewrite rule, writes a JSON response to stdout\n * that tells Claude Code to use the rewritten command instead.\n * If no rule matches, exits 0 with empty stdout (pass through unchanged).\n *\n * NON-BLOCKING GUARANTEE: This function ALWAYS exits 0.\n * A non-zero exit would cause Claude Code to block the agent's command.\n * We must never block, even on errors.\n *\n * Claude Code PreToolUse input format (stdin):\n *   { \"tool_name\": \"Bash\", \"tool_input\": { \"command\": \"grep ...\" } }\n *\n * Response format when rewriting (stdout):\n *   {\n *     \"hookSpecificOutput\": {\n *       \"hookEventName\": \"PreToolUse\",\n *       \"permissionDecision\": \"allow\",\n *       \"permissionDecisionReason\": \"...\",\n *       \"updatedInput\": { \"command\": \"code-intel search ...\" }\n *     }\n *   }\n */\n/**\n * `code-intel-hook cursor` — reads Cursor preToolUse stdin JSON, writes response JSON.\n *\n * Cursor format differs from Claude Code:\n *   Input:  { \"tool_input\": { \"command\": \"grep ...\" } }\n *   Output (rewrite): { \"permission\": \"allow\", \"updated_input\": { \"command\": \"...\" } }\n *   Output (no match): {} (Cursor requires JSON on all paths, even pass-through)\n *\n * ALWAYS exits 0 — non-blocking guarantee.\n */\n/**\n * `code-intel-hook copilot` — handles both VS Code Copilot Chat and Copilot CLI.\n *\n * Auto-detects input format:\n *   VS Code Chat:  snake_case { tool_name, tool_input: { command } }\n *                 → updatedInput (transparent rewrite)\n *   Copilot CLI:  camelCase { toolName, toolArgs: '{\"command\":\"...\"}' }\n *                 → deny-with-suggestion (CLI doesn't support updatedInput)\n *\n * ALWAYS exits 0 — non-blocking guarantee.\n */\nexport function runCopilotHook(): void {\n  process.on('uncaughtException', () => process.exit(0));\n  process.on('unhandledRejection', () => process.exit(0));\n\n  let input = '';\n  process.stdin.setEncoding('utf-8');\n  process.stdin.on('data', (chunk: string) => { input += chunk; });\n  process.stdin.on('end', () => {\n    try {\n      if (!input.trim()) { process.exit(0); }\n\n      const parsed = JSON.parse(input) as Record<string, unknown>;\n\n      // ── VS Code Copilot Chat format (snake_case) ─────────────────────────\n      // tool_name: \"runTerminalCommand\" | \"Bash\"\n      // tool_input: { command: \"...\" }\n      if (parsed.tool_name && !parsed.toolName) {\n        const toolName = parsed.tool_name as string;\n        if (!['runTerminalCommand', 'Bash', 'bash'].includes(toolName)) {\n          process.exit(0);\n        }\n        const toolInput = parsed.tool_input as Record<string, unknown> | undefined;\n        const cmd = toolInput?.command as string | undefined;\n        if (!cmd || !cmd.trim()) { process.exit(0); }\n\n        const rewritten = rewriteCommand(cmd);\n        if (rewritten === null || rewritten === cmd) { process.exit(0); }\n\n        // VS Code supports updatedInput — transparent rewrite\n        const response = {\n          hookSpecificOutput: {\n            hookEventName: 'PreToolUse',\n            permissionDecision: 'allow',\n            permissionDecisionReason: 'code-intel: semantic search replaces grep/cat',\n            updatedInput: { ...toolInput, command: rewritten },\n          },\n        };\n        process.stdout.write(JSON.stringify(response));\n        process.exit(0);\n      }\n\n      // ── Copilot CLI format (camelCase, toolArgs JSON-stringified) ─────────\n      // toolName: \"bash\"\n      // toolArgs: '{\"command\":\"...\"}'\n      if (parsed.toolName) {\n        if ((parsed.toolName as string).toLowerCase() !== 'bash') { process.exit(0); }\n        let cmd = '';\n        try {\n          const toolArgs = JSON.parse(parsed.toolArgs as string) as Record<string, unknown>;\n          cmd = (toolArgs.command as string) ?? '';\n        } catch { process.exit(0); }\n\n        if (!cmd.trim()) { process.exit(0); }\n        const rewritten = rewriteCommand(cmd);\n        if (rewritten === null || rewritten === cmd) { process.exit(0); }\n\n        // CLI doesn't support updatedInput — use deny-with-suggestion instead\n        const response = {\n          permissionDecision: 'deny',\n          permissionDecisionReason: `Use code-intel: ${rewritten}`,\n        };\n        process.stdout.write(JSON.stringify(response));\n        process.exit(0);\n      }\n\n      process.exit(0);\n    } catch {\n      process.exit(0);\n    }\n  });\n  process.stdin.on('error', () => process.exit(0));\n}\n\nexport function runCursorHook(): void {\n  process.on('uncaughtException', () => { process.stdout.write('{}'); process.exit(0); });\n  process.on('unhandledRejection', () => { process.stdout.write('{}'); process.exit(0); });\n\n  let input = '';\n  process.stdin.setEncoding('utf-8');\n  process.stdin.on('data', (chunk: string) => { input += chunk; });\n  process.stdin.on('end', () => {\n    try {\n      if (!input.trim()) { process.stdout.write('{}'); process.exit(0); }\n\n      const parsed = JSON.parse(input) as {\n        tool_input?: { command?: string; [key: string]: unknown };\n        [key: string]: unknown;\n      };\n\n      const cmd = parsed?.tool_input?.command;\n      if (typeof cmd !== 'string' || !cmd.trim()) { process.stdout.write('{}'); process.exit(0); }\n\n      const rewritten = rewriteCommand(cmd);\n      if (rewritten === null || rewritten === cmd) { process.stdout.write('{}'); process.exit(0); }\n\n      // Cursor response format: permission + updated_input (no hookSpecificOutput)\n      const response = {\n        permission: 'allow',\n        updated_input: { command: rewritten },\n      };\n      process.stdout.write(JSON.stringify(response));\n      process.exit(0);\n    } catch {\n      process.stdout.write('{}');\n      process.exit(0);\n    }\n  });\n  process.stdin.on('error', () => { process.stdout.write('{}'); process.exit(0); });\n}\n\n/**\n * `code-intel-hook gemini` — reads Gemini CLI BeforeTool stdin JSON, writes response JSON.\n *\n * Gemini format differs from Claude Code and Cursor:\n *   Input:  { \"tool_name\": \"run_shell_command\", \"tool_input\": { \"command\": \"grep ...\" } }\n *   Output (rewrite): { \"decision\": \"allow\", \"hookSpecificOutput\": { \"tool_input\": { \"command\": \"...\" } } }\n *   Output (no match): { \"decision\": \"allow\" }\n *\n * ALWAYS exits 0 — non-blocking guarantee.\n */\nexport function runGeminiHook(): void {\n  process.on('uncaughtException', () => { process.stdout.write('{\"decision\":\"allow\"}'); process.exit(0); });\n  process.on('unhandledRejection', () => { process.stdout.write('{\"decision\":\"allow\"}'); process.exit(0); });\n\n  let input = '';\n  process.stdin.setEncoding('utf-8');\n  process.stdin.on('data', (chunk: string) => { input += chunk; });\n  process.stdin.on('end', () => {\n    try {\n      if (!input.trim()) { process.stdout.write('{\"decision\":\"allow\"}'); process.exit(0); }\n\n      const parsed = JSON.parse(input) as {\n        tool_name?: string;\n        tool_input?: { command?: string; [key: string]: unknown };\n        [key: string]: unknown;\n      };\n\n      // Gemini uses tool_name = \"run_shell_command\"\n      const toolName = parsed?.tool_name;\n      if (toolName && toolName !== 'run_shell_command') {\n        process.stdout.write('{\"decision\":\"allow\"}');\n        process.exit(0);\n      }\n\n      const cmd = parsed?.tool_input?.command;\n      if (typeof cmd !== 'string' || !cmd.trim()) {\n        process.stdout.write('{\"decision\":\"allow\"}');\n        process.exit(0);\n      }\n\n      const rewritten = rewriteCommand(cmd);\n      if (rewritten === null || rewritten === cmd) {\n        process.stdout.write('{\"decision\":\"allow\"}');\n        process.exit(0);\n      }\n\n      // Gemini response format: decision + hookSpecificOutput.tool_input\n      const response = {\n        decision: 'allow',\n        hookSpecificOutput: {\n          tool_input: { command: rewritten },\n        },\n      };\n      process.stdout.write(JSON.stringify(response));\n      process.exit(0);\n    } catch {\n      process.stdout.write('{\"decision\":\"allow\"}');\n      process.exit(0);\n    }\n  });\n  process.stdin.on('error', () => { process.stdout.write('{\"decision\":\"allow\"}'); process.exit(0); });\n}\n\nexport function runClaudeHook(): void {\n  // Override any previously registered exit(1) handlers.\n  // These run before the global handlers in main.ts if anything throws\n  // before we reach the try/catch inside stdin.on('end').\n  process.on('uncaughtException', () => process.exit(0));\n  process.on('unhandledRejection', () => process.exit(0));\n\n  let input = '';\n  process.stdin.setEncoding('utf-8');\n\n  process.stdin.on('data', (chunk: string) => {\n    input += chunk;\n  });\n\n  process.stdin.on('end', () => {\n    try {\n      if (!input.trim()) {\n        process.exit(0);\n      }\n\n      // Parse the PreToolUse JSON payload\n      const parsed = JSON.parse(input) as {\n        tool_input?: { command?: string; [key: string]: unknown };\n        [key: string]: unknown;\n      };\n\n      const cmd = parsed?.tool_input?.command;\n      if (typeof cmd !== 'string' || !cmd.trim()) {\n        process.exit(0);\n      }\n\n      const rewritten = rewriteCommand(cmd);\n\n      // No match or identical → pass through (empty stdout + exit 0)\n      if (rewritten === null || rewritten === cmd) {\n        process.exit(0);\n      }\n\n      // Build the Claude Code PreToolUse response\n      const response = {\n        hookSpecificOutput: {\n          hookEventName: 'PreToolUse',\n          permissionDecision: 'allow',\n          permissionDecisionReason: 'code-intel: semantic search replaces grep/cat',\n          updatedInput: {\n            ...parsed.tool_input,\n            command: rewritten,\n          },\n        },\n      };\n\n      process.stdout.write(JSON.stringify(response));\n      process.exit(0);\n    } catch {\n      // JSON parse error, unexpected payload shape, or anything else.\n      // ALWAYS exit 0 — never block the agent's command execution.\n      process.exit(0);\n    }\n  });\n\n  process.stdin.on('error', () => {\n    process.exit(0); // stdin read error → pass through\n  });\n}\n","#!/usr/bin/env node\n/**\n * hook.ts — Tiny standalone hook entry point.\n *\n * This is compiled to dist/cli/hook.js and published as the `code-intel-hook`\n * binary. It imports ONLY hook-rewriter.ts — nothing else.\n *\n * Why separate from main.ts:\n *   main.ts bundles 714KB of OTel, DB, graph, pipeline code.\n *   Even with IS_HOOK_MODE guards, Node.js still parses the entire bundle\n *   (~850ms startup). This hook binary is ~5KB and starts in ~50ms.\n *\n * This binary is installed into ~/.claude/settings.json by `code-intel setup`:\n *   { \"command\": \"code-intel-hook claude\" }\n */\n\nimport { runClaudeHook, runCopilotHook, runCursorHook, runGeminiHook } from './hook-rewriter.js';\n\nconst agent = process.argv[2];\n\nif (!agent) {\n  process.stderr.write('[code-intel-hook] Usage: code-intel-hook <agent>\\n');\n  process.stderr.write('  Agents: claude, copilot, cursor, gemini\\n');\n  process.exit(0);\n}\n\nswitch (agent) {\n  case 'claude':\n    runClaudeHook();\n    break;\n  case 'copilot':\n    runCopilotHook();\n    break;\n  case 'cursor':\n    runCursorHook();\n    break;\n  case 'gemini':\n    runGeminiHook();\n    break;\n  default:\n    process.stderr.write(`[code-intel-hook] Unknown agent: ${agent}\\n`);\n    process.exit(0);\n}\n"]}
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* hook-rewriter.ts\n *\n * Single source of truth for all command rewrite rules and agent hook handlers.\n *\n * Called by:\n *   - `code-intel rewrite <cmd>`  → exit 0 (match) | exit 1 (no match)\n *   - `code-intel hook claude`    → reads stdin PreToolUse/PostToolUse JSON, writes response JSON\n *   - `code-intel hook cursor`    → same, Cursor format\n *   - `code-intel hook gemini`    → same, Gemini format\n *   - `code-intel hook copilot`   → same, Copilot format\n *\n * ZERO heavy imports — this module must load in <50ms.\n * Filesystem access and spawnSync are allowed only in hook handlers (not in rewriteCommand).\n *\n * Hook behaviour (inspired by GitNexus plugin pattern):\n *   PreToolUse  — rewrites grep/rg/cat to code-intel equivalents; optionally injects\n *                 graph context as `additionalContext` via `code-intel augment`.\n *   PostToolUse — detects stale knowledge graph after git mutations (commit/merge/rebase/\n *                 cherry-pick/pull) by comparing `git rev-parse HEAD` against the\n *                 commitHash stored in `.code-intel/meta.json`. Notifies the agent to\n *                 re-run `code-intel analyze` when the index is behind.\n */\n\nimport process from 'node:process';\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport { spawnSync } from 'node:child_process';\n\n// ─── Stale-index detection helpers ───────────────────────────────────────────\n\n/**\n * Walk up the directory tree from startDir looking for a `.code-intel/` directory.\n * Returns the path to `.code-intel/` or null if not found (up to 8 levels).\n */\nfunction findCodeIntelDir(startDir: string): string | null {\n  let dir = startDir;\n  for (let i = 0; i < 8; i++) {\n    const candidate = path.join(dir, '.code-intel');\n    try { if (fs.statSync(candidate).isDirectory()) return candidate; } catch { /* continue */ }\n    const parent = path.dirname(dir);\n    if (parent === dir) break;\n    dir = parent;\n  }\n  return null;\n}\n\n/** Read the `commitHash` stored in `.code-intel/meta.json` (empty string if absent). */\nfunction loadIndexedCommit(codeIntelDir: string): string {\n  try {\n    const meta = JSON.parse(fs.readFileSync(path.join(codeIntelDir, 'meta.json'), 'utf-8')) as Record<string, unknown>;\n    return (meta.commitHash as string) ?? '';\n  } catch { return ''; }\n}\n\n/** Run `git rev-parse HEAD` synchronously (empty string on error). */\nfunction getHeadCommit(cwd: string): string {\n  try {\n    const r = spawnSync('git', ['rev-parse', 'HEAD'], {\n      encoding: 'utf-8', timeout: 3000, cwd,\n      stdio: ['pipe', 'pipe', 'pipe'],\n    });\n    return (r.stdout ?? '').trim();\n  } catch { return ''; }\n}\n\n// ─── Augment helper ───────────────────────────────────────────────────────────\n\n/**\n * Spawn `code-intel augment -- <pattern>` synchronously and return its stdout.\n * Falls back to npx if the binary is not on PATH.\n * Returns empty string on any error — this must never block the agent.\n *\n * SECURITY: args are passed as array elements, never through shell interpolation.\n */\nfunction runCodeIntelAugment(pattern: string, cwd: string): string {\n  const isWin = process.platform === 'win32';\n  const bin   = isWin ? 'code-intel.cmd' : 'code-intel';\n  const npxBin = isWin ? 'npx.cmd' : 'npx';\n\n  let r = spawnSync(bin, ['augment', '--', pattern], {\n    encoding: 'utf-8', timeout: 6000, cwd,\n    stdio: ['pipe', 'pipe', 'pipe'],\n  });\n  if (r.error || r.status !== 0) {\n    r = spawnSync(npxBin, ['code-intel', 'augment', '--', pattern], {\n      encoding: 'utf-8', timeout: 10000, cwd,\n      stdio: ['pipe', 'pipe', 'pipe'],\n    });\n  }\n  return (!r.error && r.status === 0) ? (r.stdout ?? '').trim() : '';\n}\n\n// ─── PostToolUse handler ──────────────────────────────────────────────────────\n\n/**\n * PostToolUse: after git mutations, check whether the knowledge graph is stale.\n *\n * Instead of running a full `code-intel analyze` synchronously (which would block\n * the agent for up to 120s), we do a lightweight check: compare `git rev-parse HEAD`\n * against the `commitHash` stored in `.code-intel/meta.json`. When they differ, we\n * notify the agent via `additionalContext` so it can decide when to reindex.\n *\n * Writes the response JSON to stdout (empty string → no output / pass through).\n */\nfunction handlePostToolUse(input: Record<string, unknown>): void {\n  const toolName = (input.tool_name as string | undefined) ?? '';\n  if (toolName !== 'Bash') return;\n\n  const command = ((input.tool_input as Record<string, unknown> | undefined)?.command as string | undefined) ?? '';\n  // Only care about git operations that advance HEAD\n  if (!/\\bgit\\s+(commit|merge|rebase|cherry-pick|pull)(\\s|$)/.test(command)) return;\n\n  // Ignore failed commands\n  const exitCode = (input.tool_output as Record<string, unknown> | undefined)?.exit_code;\n  if (exitCode !== undefined && exitCode !== 0) return;\n\n  const cwd = (input.cwd as string | undefined) ?? process.cwd();\n  if (!path.isAbsolute(cwd)) return;\n\n  const codeIntelDir = findCodeIntelDir(cwd);\n  if (!codeIntelDir) return;  // no index for this repo → nothing to check\n\n  const head = getHeadCommit(cwd);\n  if (!head) return;\n\n  const indexed = loadIndexedCommit(codeIntelDir);\n  if (head && head === indexed) return;  // index is current → nothing to notify\n\n  const since   = indexed ? indexed.slice(0, 7) : 'never';\n  const current = head.slice(0, 7);\n  const msg =\n    `code-intel index is stale (last indexed: ${since}, current HEAD: ${current}). ` +\n    `Run \\`code-intel analyze\\` to update the knowledge graph.`;\n\n  process.stdout.write(\n    JSON.stringify({ hookSpecificOutput: { hookEventName: 'PostToolUse', additionalContext: msg } }),\n  );\n}\n\n// ─── Source file extensions ───────────────────────────────────────────────────\n// Only these are worth inspecting via code-intel inspect.\n// All other file types (config, docs, logs, data) pass through unchanged.\n\nconst SOURCE_EXT = new Set([\n  'ts', 'tsx', 'js', 'jsx', 'mjs', 'cjs',\n  'py', 'pyi',\n  'rs',\n  'go',\n  'java', 'kt', 'kts',\n  'rb',\n  'cs',\n  'cpp', 'cc', 'cxx', 'c', 'h', 'hpp',\n  'swift',\n  'scala',\n  'php',\n]);\n\n// ─── Helpers ──────────────────────────────────────────────────────────────────\n\n/**\n * Regex metacharacters that indicate a true regex pattern, not a symbol name.\n * If a grep/rg search term contains any of these, we don't rewrite.\n */\nconst REGEX_META_RE = /[.*+?^${}()|[\\]\\\\]/;\n\n/**\n * A \"symbol-like\" identifier: starts with letter/$/_,\n * followed by alphanumeric/$/_/./- characters.\n * CamelCase, snake_case, dot.notation all qualify.\n */\nconst SYMBOL_ID_RE = /^[A-Za-z_$][A-Za-z0-9_$.-]*$/;\n\nfunction isSymbolLike(term: string): boolean {\n  return SYMBOL_ID_RE.test(term) && !REGEX_META_RE.test(term);\n}\n\nfunction isSourceFile(filePath: string): boolean {\n  const dot = filePath.lastIndexOf('.');\n  if (dot === -1) return false;\n  return SOURCE_EXT.has(filePath.slice(dot + 1).toLowerCase());\n}\n\n/** Extract the filename stem (basename without extension). */\nfunction fileStem(filePath: string): string {\n  const base = filePath.includes('/')\n    ? filePath.slice(filePath.lastIndexOf('/') + 1)\n    : filePath;\n  const dot = base.lastIndexOf('.');\n  return dot === -1 ? base : base.slice(0, dot);\n}\n\n/**\n * Extract a symbol-like search term from a grep or rg command.\n * Returns null if:\n *   - The term looks like a regex (contains metacharacters)\n *   - The flags indicate non-symbol-discovery use (-c, -v, -l, -L, -o, -Z)\n *   - No clear search term can be identified\n *\n * Flags that trigger passthrough (not symbol search):\n *   -c  count matches per file\n *   -v  invert match (select non-matching lines)\n *   -l  list files that have matches\n *   -L  list files that have NO matches\n *   -o  print only the matching part\n *   -Z  use NUL byte as line separator\n */\nfunction extractGrepSymbol(cmd: string): string | null {\n  // Reject if any flag group contains a non-symbol-discovery flag character.\n  // This regex looks for a dash followed by any combo of letters containing c/v/l/L/o/Z.\n  // We use a word-boundary aware pattern: -rnic is ok (r,n,i,I are fine),\n  // -rnc is not (c = count). The flag can appear anywhere after the command name.\n  if (/(?:^|\\s)-[a-zA-Z]*[cvlLoZ]/.test(cmd)) return null;\n\n  // Try double-quoted or single-quoted term first: grep \"Symbol\" or grep 'Symbol'\n  const quoted = cmd.match(/(?:^|\\s)[\"']([^\"']+)[\"'](?:\\s|$)/);\n  if (quoted) {\n    const term = quoted[1];\n    return isSymbolLike(term) ? term : null;\n  }\n\n  // Try unquoted term: skip command name and flags to find first bare identifier\n  const tokens = cmd.split(/\\s+/).slice(1); // skip 'grep' or 'rg'\n  for (const tok of tokens) {\n    if (tok.startsWith('-')) continue;                      // skip flags\n    if (tok.startsWith('/')) continue;                      // skip absolute paths\n    if (tok.startsWith('./') || tok.startsWith('../')) continue; // skip relative paths\n    if (tok.includes('/')) continue;                        // skip paths with slashes\n    if (tok === '.' || tok === '..') continue;              // skip dir shortcuts\n    // First non-flag, non-path token is the search pattern\n    return isSymbolLike(tok) ? tok : null;\n  }\n\n  return null;\n}\n\n// ─── Core rewrite function ────────────────────────────────────────────────────\n\n/**\n * Attempt to rewrite `cmd` to its code-intel equivalent.\n *\n * Returns the rewritten command string, or null if no rule matched.\n * NEVER throws — all rule errors silently degrade to null (passthrough).\n */\nexport function rewriteCommand(cmd: string): string | null {\n  try {\n    const trimmed = cmd.trim();\n    if (!trimmed) return null;\n\n    // ── Guard 1: Already a code-intel command (idempotency + anti-loop) ──────\n    // This prevents: code-intel search \"X\" → being rewritten again.\n    if (trimmed.startsWith('code-intel ') || trimmed === 'code-intel') return null;\n\n    // ── Guard 2: Compound commands — pass through in v1 ──────────────────────\n    // We don't attempt to split && || ; | in v1.\n    // A simple character scan is safe here since we check before any rule matching.\n    if (/(?:&&|\\|\\||;|\\|)/.test(trimmed)) return null;\n\n    // ── Rule 1: grep → code-intel search ─────────────────────────────────────\n    if (/^grep\\s/.test(trimmed)) {\n      const sym = extractGrepSymbol(trimmed);\n      if (sym) return `code-intel search \"${sym}\"`;\n      return null;\n    }\n\n    // ── Rule 2: rg → code-intel search ───────────────────────────────────────\n    if (/^rg\\s/.test(trimmed)) {\n      // Reject rg-specific structural flags (not symbol search)\n      if (/\\s--files(?:\\s|$)/.test(trimmed)) return null;\n      if (/\\s--files-with-matches(?:\\s|$)/.test(trimmed)) return null;\n      if (/\\s--type-not\\b/.test(trimmed)) return null;\n      const sym = extractGrepSymbol(trimmed);\n      if (sym) return `code-intel search \"${sym}\"`;\n      return null;\n    }\n\n    // ── Rule 3: cat <single-source-file> → code-intel inspect <stem> ─────────\n    if (/^cat\\s/.test(trimmed)) {\n      // Must be exactly: cat <one-token> — no multi-file, no options\n      const m = trimmed.match(/^cat\\s+(\\S+)$/);\n      if (!m) return null;           // multi-file or flags present\n      const filePath = m[1];\n      if (filePath === '-') return null;           // stdin passthrough\n      if (filePath.startsWith('>')) return null;   // write redirect\n      if (!isSourceFile(filePath)) return null;    // not a source file\n      return `code-intel inspect ${fileStem(filePath)}`;\n    }\n\n    // ── Rule 4: head/tail <single-source-file> → code-intel inspect <stem> ───\n    if (/^(?:head|tail)\\s/.test(trimmed)) {\n      if (/\\s-f\\b/.test(trimmed)) return null;     // tail -f = live follow, not inspection\n      // Accept common forms:\n      //   head <file>\n      //   head -N <file>\n      //   head -n N <file>\n      //   head --lines=N <file>\n      const m = trimmed.match(\n        /^(?:head|tail)\\s+(?:-\\d+\\s+|-n\\s+\\d+\\s+|--lines=\\d+\\s+)?(\\S+)$/,\n      );\n      if (!m) return null;\n      const filePath = m[1];\n      if (!isSourceFile(filePath)) return null;\n      return `code-intel inspect ${fileStem(filePath)}`;\n    }\n\n    return null;\n  } catch {\n    // Any unexpected error → silently pass through.\n    // A rule must NEVER cause the hook to crash.\n    return null;\n  }\n}\n\n// ─── CLI: `code-intel rewrite <cmd>` ─────────────────────────────────────────\n\n/**\n * Entry point for `code-intel rewrite <cmd>`.\n *\n * Exit codes (mirrors RTK exit code protocol):\n *   0 + stdout  → rewrite found; hook may auto-allow the rewritten command\n *   1           → no match; hook passes through unchanged\n */\nexport function runRewrite(cmd: string): never {\n  const rewritten = rewriteCommand(cmd.trim());\n  if (rewritten === null) {\n    process.exit(1);\n  }\n  process.stdout.write(rewritten);\n  process.exit(0);\n}\n\n// ─── CLI: `code-intel hook claude` ───────────────────────────────────────────\n\n/**\n * Entry point for `code-intel hook claude`.\n *\n * Reads a Claude Code PreToolUse JSON payload from stdin.\n * If the command matches a rewrite rule, writes a JSON response to stdout\n * that tells Claude Code to use the rewritten command instead.\n * If no rule matches, exits 0 with empty stdout (pass through unchanged).\n *\n * NON-BLOCKING GUARANTEE: This function ALWAYS exits 0.\n * A non-zero exit would cause Claude Code to block the agent's command.\n * We must never block, even on errors.\n *\n * Claude Code PreToolUse input format (stdin):\n *   { \"tool_name\": \"Bash\", \"tool_input\": { \"command\": \"grep ...\" } }\n *\n * Response format when rewriting (stdout):\n *   {\n *     \"hookSpecificOutput\": {\n *       \"hookEventName\": \"PreToolUse\",\n *       \"permissionDecision\": \"allow\",\n *       \"permissionDecisionReason\": \"...\",\n *       \"updatedInput\": { \"command\": \"code-intel search ...\" }\n *     }\n *   }\n */\n/**\n * `code-intel-hook cursor` — reads Cursor preToolUse stdin JSON, writes response JSON.\n *\n * Cursor format differs from Claude Code:\n *   Input:  { \"tool_input\": { \"command\": \"grep ...\" } }\n *   Output (rewrite): { \"permission\": \"allow\", \"updated_input\": { \"command\": \"...\" } }\n *   Output (no match): {} (Cursor requires JSON on all paths, even pass-through)\n *\n * ALWAYS exits 0 — non-blocking guarantee.\n */\n/**\n * `code-intel-hook copilot` — handles both VS Code Copilot Chat and Copilot CLI.\n *\n * Auto-detects input format:\n *   VS Code Chat:  snake_case { tool_name, tool_input: { command } }\n *                 → updatedInput (transparent rewrite)\n *   Copilot CLI:  camelCase { toolName, toolArgs: '{\"command\":\"...\"}' }\n *                 → deny-with-suggestion (CLI doesn't support updatedInput)\n *\n * ALWAYS exits 0 — non-blocking guarantee.\n */\nexport function runCopilotHook(): void {\n  process.on('uncaughtException', () => process.exit(0));\n  process.on('unhandledRejection', () => process.exit(0));\n\n  let input = '';\n  process.stdin.setEncoding('utf-8');\n  process.stdin.on('data', (chunk: string) => { input += chunk; });\n  process.stdin.on('end', () => {\n    try {\n      if (!input.trim()) { process.exit(0); }\n\n      const parsed = JSON.parse(input) as Record<string, unknown>;\n\n      // ── VS Code Copilot Chat format (snake_case) ─────────────────────────\n      // tool_name: \"runTerminalCommand\" | \"Bash\"\n      // tool_input: { command: \"...\" }\n      if (parsed.tool_name && !parsed.toolName) {\n        const toolName = parsed.tool_name as string;\n        if (!['runTerminalCommand', 'Bash', 'bash'].includes(toolName)) {\n          process.exit(0);\n        }\n        const toolInput = parsed.tool_input as Record<string, unknown> | undefined;\n        const cmd = toolInput?.command as string | undefined;\n        if (!cmd || !cmd.trim()) { process.exit(0); }\n\n        const rewritten = rewriteCommand(cmd);\n        if (rewritten === null || rewritten === cmd) { process.exit(0); }\n\n        // VS Code supports updatedInput — transparent rewrite\n        const response = {\n          hookSpecificOutput: {\n            hookEventName: 'PreToolUse',\n            permissionDecision: 'allow',\n            permissionDecisionReason: 'code-intel: semantic search replaces grep/cat',\n            updatedInput: { ...toolInput, command: rewritten },\n          },\n        };\n        process.stdout.write(JSON.stringify(response));\n        process.exit(0);\n      }\n\n      // ── Copilot CLI format (camelCase, toolArgs JSON-stringified) ─────────\n      // toolName: \"bash\"\n      // toolArgs: '{\"command\":\"...\"}'\n      if (parsed.toolName) {\n        if ((parsed.toolName as string).toLowerCase() !== 'bash') { process.exit(0); }\n        let cmd = '';\n        try {\n          const toolArgs = JSON.parse(parsed.toolArgs as string) as Record<string, unknown>;\n          cmd = (toolArgs.command as string) ?? '';\n        } catch { process.exit(0); }\n\n        if (!cmd.trim()) { process.exit(0); }\n        const rewritten = rewriteCommand(cmd);\n        if (rewritten === null || rewritten === cmd) { process.exit(0); }\n\n        // CLI doesn't support updatedInput — use deny-with-suggestion instead\n        const response = {\n          permissionDecision: 'deny',\n          permissionDecisionReason: `Use code-intel: ${rewritten}`,\n        };\n        process.stdout.write(JSON.stringify(response));\n        process.exit(0);\n      }\n\n      process.exit(0);\n    } catch {\n      process.exit(0);\n    }\n  });\n  process.stdin.on('error', () => process.exit(0));\n}\n\nexport function runCursorHook(): void {\n  process.on('uncaughtException', () => { process.stdout.write('{}'); process.exit(0); });\n  process.on('unhandledRejection', () => { process.stdout.write('{}'); process.exit(0); });\n\n  let input = '';\n  process.stdin.setEncoding('utf-8');\n  process.stdin.on('data', (chunk: string) => { input += chunk; });\n  process.stdin.on('end', () => {\n    try {\n      if (!input.trim()) { process.stdout.write('{}'); process.exit(0); }\n\n      const parsed = JSON.parse(input) as {\n        tool_input?: { command?: string; [key: string]: unknown };\n        [key: string]: unknown;\n      };\n\n      const cmd = parsed?.tool_input?.command;\n      if (typeof cmd !== 'string' || !cmd.trim()) { process.stdout.write('{}'); process.exit(0); }\n\n      const rewritten = rewriteCommand(cmd);\n      if (rewritten === null || rewritten === cmd) { process.stdout.write('{}'); process.exit(0); }\n\n      // Cursor response format: permission + updated_input (no hookSpecificOutput)\n      const response = {\n        permission: 'allow',\n        updated_input: { command: rewritten },\n      };\n      process.stdout.write(JSON.stringify(response));\n      process.exit(0);\n    } catch {\n      process.stdout.write('{}');\n      process.exit(0);\n    }\n  });\n  process.stdin.on('error', () => { process.stdout.write('{}'); process.exit(0); });\n}\n\n/**\n * `code-intel-hook gemini` — reads Gemini CLI BeforeTool stdin JSON, writes response JSON.\n *\n * Gemini format differs from Claude Code and Cursor:\n *   Input:  { \"tool_name\": \"run_shell_command\", \"tool_input\": { \"command\": \"grep ...\" } }\n *   Output (rewrite): { \"decision\": \"allow\", \"hookSpecificOutput\": { \"tool_input\": { \"command\": \"...\" } } }\n *   Output (no match): { \"decision\": \"allow\" }\n *\n * ALWAYS exits 0 — non-blocking guarantee.\n */\nexport function runGeminiHook(): void {\n  process.on('uncaughtException', () => { process.stdout.write('{\"decision\":\"allow\"}'); process.exit(0); });\n  process.on('unhandledRejection', () => { process.stdout.write('{\"decision\":\"allow\"}'); process.exit(0); });\n\n  let input = '';\n  process.stdin.setEncoding('utf-8');\n  process.stdin.on('data', (chunk: string) => { input += chunk; });\n  process.stdin.on('end', () => {\n    try {\n      if (!input.trim()) { process.stdout.write('{\"decision\":\"allow\"}'); process.exit(0); }\n\n      const parsed = JSON.parse(input) as {\n        tool_name?: string;\n        tool_input?: { command?: string; [key: string]: unknown };\n        [key: string]: unknown;\n      };\n\n      // Gemini uses tool_name = \"run_shell_command\"\n      const toolName = parsed?.tool_name;\n      if (toolName && toolName !== 'run_shell_command') {\n        process.stdout.write('{\"decision\":\"allow\"}');\n        process.exit(0);\n      }\n\n      const cmd = parsed?.tool_input?.command;\n      if (typeof cmd !== 'string' || !cmd.trim()) {\n        process.stdout.write('{\"decision\":\"allow\"}');\n        process.exit(0);\n      }\n\n      const rewritten = rewriteCommand(cmd);\n      if (rewritten === null || rewritten === cmd) {\n        process.stdout.write('{\"decision\":\"allow\"}');\n        process.exit(0);\n      }\n\n      // Gemini response format: decision + hookSpecificOutput.tool_input\n      const response = {\n        decision: 'allow',\n        hookSpecificOutput: {\n          tool_input: { command: rewritten },\n        },\n      };\n      process.stdout.write(JSON.stringify(response));\n      process.exit(0);\n    } catch {\n      process.stdout.write('{\"decision\":\"allow\"}');\n      process.exit(0);\n    }\n  });\n  process.stdin.on('error', () => { process.stdout.write('{\"decision\":\"allow\"}'); process.exit(0); });\n}\n\nexport function runClaudeHook(): void {\n  // Override any previously registered exit(1) handlers.\n  // These run before the global handlers in main.ts if anything throws\n  // before we reach the try/catch inside stdin.on('end').\n  process.on('uncaughtException', () => process.exit(0));\n  process.on('unhandledRejection', () => process.exit(0));\n\n  let input = '';\n  process.stdin.setEncoding('utf-8');\n\n  process.stdin.on('data', (chunk: string) => {\n    input += chunk;\n  });\n\n  process.stdin.on('end', () => {\n    try {\n      if (!input.trim()) { process.exit(0); }\n\n      const parsed = JSON.parse(input) as Record<string, unknown>;\n      const hookEvent = (parsed.hook_event_name as string | undefined) ?? 'PreToolUse';\n\n      // ── PostToolUse: stale-index notification after git mutations ──────────\n      if (hookEvent === 'PostToolUse') {\n        handlePostToolUse(parsed);\n        process.exit(0);\n      }\n\n      // ── PreToolUse: command rewrite + optional graph context augment ───────\n      const toolInput = parsed.tool_input as Record<string, unknown> | undefined;\n      const cmd = toolInput?.command;\n      if (typeof cmd !== 'string' || !cmd.trim()) { process.exit(0); }\n\n      const rewritten = rewriteCommand(cmd);\n      const cwd = (parsed.cwd as string | undefined) ?? process.cwd();\n\n      // Try to augment with graph context (non-blocking — any error → skip)\n      let additionalContext: string | undefined;\n      try {\n        if (path.isAbsolute(cwd) && findCodeIntelDir(cwd)) {\n          const pattern = extractGrepSymbol(cmd) ?? (rewritten ? undefined : undefined);\n          if (pattern) {\n            const ctx = runCodeIntelAugment(pattern, cwd);\n            if (ctx) additionalContext = ctx;\n          }\n        }\n      } catch { /* ignore augment errors */ }\n\n      if (rewritten !== null && rewritten !== cmd) {\n        // Rewrite found — update input command and optionally add context\n        const response: Record<string, unknown> = {\n          hookSpecificOutput: {\n            hookEventName: 'PreToolUse',\n            permissionDecision: 'allow',\n            permissionDecisionReason: 'code-intel: semantic search replaces grep/cat',\n            updatedInput: { ...toolInput, command: rewritten },\n            ...(additionalContext ? { additionalContext } : {}),\n          },\n        };\n        process.stdout.write(JSON.stringify(response));\n      } else if (additionalContext) {\n        // No rewrite but we have graph context to inject\n        const response = {\n          hookSpecificOutput: {\n            hookEventName: 'PreToolUse',\n            additionalContext,\n          },\n        };\n        process.stdout.write(JSON.stringify(response));\n      }\n      // else: no rewrite, no context → empty stdout = pass through\n\n      process.exit(0);\n    } catch {\n      // JSON parse error, unexpected payload shape, or anything else.\n      // ALWAYS exit 0 — never block the agent's command execution.\n      process.exit(0);\n    }\n  });\n\n  process.stdin.on('error', () => { process.exit(0); });\n}\n","#!/usr/bin/env node\n/**\n * hook.ts — Tiny standalone hook entry point.\n *\n * This is compiled to dist/cli/hook.js and published as the `code-intel-hook`\n * binary. It imports ONLY hook-rewriter.ts — nothing else.\n *\n * Why separate from main.ts:\n *   main.ts bundles 714KB of OTel, DB, graph, pipeline code.\n *   Even with IS_HOOK_MODE guards, Node.js still parses the entire bundle\n *   (~850ms startup). This hook binary is ~5KB and starts in ~50ms.\n *\n * This binary is installed into ~/.claude/settings.json by `code-intel setup`:\n *   { \"command\": \"code-intel-hook claude\" }\n */\n\nimport { runClaudeHook, runCopilotHook, runCursorHook, runGeminiHook } from './hook-rewriter.js';\n\nconst agent = process.argv[2];\n\nif (!agent) {\n  process.stderr.write('[code-intel-hook] Usage: code-intel-hook <agent>\\n');\n  process.stderr.write('  Agents: claude, copilot, cursor, gemini\\n');\n  process.exit(0);\n}\n\nswitch (agent) {\n  case 'claude':\n    runClaudeHook();\n    break;\n  case 'copilot':\n    runCopilotHook();\n    break;\n  case 'cursor':\n    runCursorHook();\n    break;\n  case 'gemini':\n    runGeminiHook();\n    break;\n  default:\n    process.stderr.write(`[code-intel-hook] Unknown agent: ${agent}\\n`);\n    process.exit(0);\n}\n"]}