feat(hooks): add config protection hook to block linter config manipulation (#758)

* feat(hooks): add config protection hook to block linter config manipulation

Agents frequently modify linter/formatter configs (.eslintrc, biome.json,
.prettierrc, .ruff.toml, etc.) to make checks pass instead of fixing
the actual code.

This PreToolUse hook intercepts Write/Edit/MultiEdit calls targeting
known config files and blocks them with a steering message that directs
the agent to fix the source code instead.

Covers: ESLint, Prettier, Biome, Ruff, ShellCheck, Stylelint, and
Markdownlint configs.

Fixes #733

* Address review: fix dead code, add missing configs, export run()

- Removed pyproject.toml from PROTECTED_FILES (was dead code since
  it was also in PARTIAL_CONFIG_FILES). Added comment explaining why
  it's intentionally excluded.
- Removed PARTIAL_CONFIG_FILES entirely (no longer needed).
- Added missing ESLint v9 TypeScript flat configs: eslint.config.ts,
  eslint.config.mts, eslint.config.cts
- Added missing Prettier ESM config: prettier.config.mjs
- Exported run() function for in-process execution via run-with-flags,
  avoiding the spawnSync overhead (~50-100ms per call).

* Handle stdin truncation gracefully, log warning instead of fail-open

If stdin exceeds 1MB, the JSON would be malformed and the catch
block would silently pass through. Now we detect truncation and
log a warning. The in-process run() path is not affected.

scripts/hooks/config-protection.js

@@ -0,0 +1,125 @@
+#!/usr/bin/env node
+/**
+ * Config Protection Hook
+ *
+ * Blocks modifications to linter/formatter config files.
+ * Agents frequently modify these to make checks pass instead of fixing
+ * the actual code. This hook steers the agent back to fixing the source.
+ *
+ * Exit codes:
+ *   0 = allow (not a config file)
+ *   2 = block (config file modification attempted)
+ */
+
+'use strict';
+
+const path = require('path');
+
+const MAX_STDIN = 1024 * 1024;
+let raw = '';
+
+const PROTECTED_FILES = new Set([
+  // ESLint (legacy + v9 flat config, JS/TS/MJS/CJS)
+  '.eslintrc',
+  '.eslintrc.js',
+  '.eslintrc.cjs',
+  '.eslintrc.json',
+  '.eslintrc.yml',
+  '.eslintrc.yaml',
+  'eslint.config.js',
+  'eslint.config.mjs',
+  'eslint.config.cjs',
+  'eslint.config.ts',
+  'eslint.config.mts',
+  'eslint.config.cts',
+  // Prettier (all config variants including ESM)
+  '.prettierrc',
+  '.prettierrc.js',
+  '.prettierrc.cjs',
+  '.prettierrc.json',
+  '.prettierrc.yml',
+  '.prettierrc.yaml',
+  'prettier.config.js',
+  'prettier.config.cjs',
+  'prettier.config.mjs',
+  // Biome
+  'biome.json',
+  'biome.jsonc',
+  // Ruff (Python)
+  '.ruff.toml',
+  'ruff.toml',
+  // Note: pyproject.toml is intentionally NOT included here because it
+  // contains project metadata alongside linter config. Blocking all edits
+  // to pyproject.toml would prevent legitimate dependency changes.
+  // Shell / Style / Markdown
+  '.shellcheckrc',
+  '.stylelintrc',
+  '.stylelintrc.json',
+  '.stylelintrc.yml',
+  '.markdownlint.json',
+  '.markdownlint.yaml',
+  '.markdownlintrc',
+]);
+
+/**
+ * Exportable run() for in-process execution via run-with-flags.js.
+ * Avoids the ~50-100ms spawnSync overhead when available.
+ */
+function run(input) {
+  const filePath = input?.tool_input?.file_path || input?.tool_input?.file || '';
+  if (!filePath) return { exitCode: 0 };
+
+  const basename = path.basename(filePath);
+  if (PROTECTED_FILES.has(basename)) {
+    return {
+      exitCode: 2,
+      stderr:
+        `BLOCKED: Modifying ${basename} is not allowed. ` +
+        `Fix the source code to satisfy linter/formatter rules instead of ` +
+        `weakening the config. If this is a legitimate config change, ` +
+        `disable the config-protection hook temporarily.`,
+    };
+  }
+
+  return { exitCode: 0 };
+}
+
+module.exports = { run };
+
+// Stdin fallback for spawnSync execution
+let truncated = false;
+process.stdin.setEncoding('utf8');
+process.stdin.on('data', chunk => {
+  if (raw.length < MAX_STDIN) {
+    const remaining = MAX_STDIN - raw.length;
+    raw += chunk.substring(0, remaining);
+    if (chunk.length > remaining) truncated = true;
+  } else {
+    truncated = true;
+  }
+});
+
+process.stdin.on('end', () => {
+  // If stdin was truncated, the JSON is likely malformed. Fail open but
+  // log a warning so the issue is visible. The run() path (used by
+  // run-with-flags.js in-process) is not affected by this.
+  if (truncated) {
+    process.stderr.write('[config-protection] Warning: stdin exceeded 1MB, skipping check\n');
+    process.stdout.write(raw);
+    return;
+  }
+
+  try {
+    const input = raw.trim() ? JSON.parse(raw) : {};
+    const result = run(input);
+
+    if (result.exitCode === 2) {
+      process.stderr.write(result.stderr + '\n');
+      process.exit(2);
+    }
+  } catch {
+    // Keep hook non-blocking on parse errors.
+  }
+
+  process.stdout.write(raw);
+});