fix(hooks): include configured hooks in scoped reads

what changed: Scoped core.hooksPath reads now request Git include expansion. A disposable global-config fixture covers ordinary includes and gitdir conditional includes through preview, install, recorded hand-on and uninstall restoration.

why: Git defaults scoped config reads to excludes, so a configured hooks folder was reported as unset and lost from the hand-on record. Request the effective included value with the existing scoped reader. No alternative design was set aside.

what it touched: machine.mjs, doctor tests, architecture map, changelog and research-kit README inventory. Writes still use the existing Git config writer.

what you verified: verified - red-first 66 passes and one expected include-read failure; then 90 doctor/machine tests passed with zero failures. Handoff OK and preflight PASS in this checkout. The required full offline suite runs in the commit gate before acceptance. Git's config documentation confirms scoped reads need --includes.

what you got wrong and fixed: mistake - the conditional-include fixture used the temporary path spelling rather than the real Git directory. where - doctor.test.mjs includeIf pattern. impact - the first Windows CI run failed on its RUNNER~1 short home alias; the --includes fix passed the other platforms and local checks. cause - Git matched the canonical directory while the fixture named its short alias. fix - build the conditional pattern from fs.realpathSync(repo). verified - 90 doctor/machine tests passed locally in 95.9 seconds; the corrected commit reruns the required full gate and supported CI before completion.

Author: StepenkoAnatoli

CHANGELOG.md

@@ -4,6 +4,8 @@ Each release of Research-Kit, newest first. The version is `KIT_VERSION` in
 `research-kit/lib/core.mjs`; a release is tagged `v<version>` (ADR-0116).
 
 ## Unreleased
+
+- Scoped hooksPath reads expand Git include and includeIf directives, preserving the previous hooks folder through installation and removal (#369).
 - Fixed `AGENTS.md` corpus description to use evergreen relative references rather than stale hardcoded entry counts (#299).
 
 - The suite's "every CLI refuses a flag it does not know" table now covers `measure`,

docs/ARCHITECTURE.md

@@ -563,7 +563,7 @@ node research-kit/bin/selftest.mjs            # all of it
 node research-kit/bin/selftest.mjs gate hook  # just these files
 ```
 
-1789 tests, offline, no key and no network. The runner **awaits** every test, so `ok` means
+1790 tests, offline, no key and no network. The runner **awaits** every test, so `ok` means
 the assertions settled (ADR-0021), and each test is raced against a watchdog
 (`RESEARCH_KIT_TEST_TIMEOUT`, default 60s).
 

research-kit/README.md

@@ -357,7 +357,7 @@ export function gitVersion(opts = {}) {
 /** Scope-aware readers: which hooksPath is set where. */
 export function hooksPath(scope = 'global', opts = {}) {
   const flag = { global: '--global', local: '--local', system: '--system' }[scope] ?? '--global';
-  return git(['config', flag, '--get', 'core.hooksPath'], opts);
+  return git(['config', flag, '--includes', '--get', 'core.hooksPath'], opts);
 }
 
 export function hooksPathEffective(opts = {}) {

research-kit/lib/machine.mjs

@@ -7,7 +7,7 @@ import { TESTED_CLI_VERSION } from '../lib/firecrawl.mjs';
 import { PATHS, resolve, readText, writeText, readJson } from '../lib/core.mjs';
 import { runDoctor, machineHealth, gateHealth, editGateState, scanForSecrets } from '../lib/doctor.mjs';
 import { installEditGate, removeEditGate, installCommitGate, removeCommitGate, settingsState, retiredRepairNote, MATCHER } from '../lib/installer.mjs';
-import { EDIT_GATE_HOOK, RETIRED_EDIT_GATE_HOOKS } from '../lib/machine.mjs';
+import { EDIT_GATE_HOOK, RETIRED_EDIT_GATE_HOOKS, hooksPath, previousHooksPath } from '../lib/machine.mjs';
 
 describe('doctor');
 
@@ -26,6 +26,39 @@ function machine({ config = {}, settings = undefined } = {}) {
 
 const find = (findings, name) => findings.find((f) => f.name === name);
 
+test('included global hooks are recorded, preserved and restored by the commit-gate install', () => {
+  requireGit('global include-based hooks');
+  for (const conditional of [false, true]) {
+    const { dir, env } = machine();
+    const repo = path.join(dir, 'repo');
+    fs.mkdirSync(repo);
+    const globalFile = path.join(dir, 'gitconfig');
+    const gitPaths = { cwd: repo, env: { ...env, GIT_CONFIG_GLOBAL: globalFile, GIT_CONFIG_NOSYSTEM: '1' } };
+    const initialized = spawnSync('git', fixtureInitArgs(repo), { env: gitPaths.env, encoding: 'utf8', windowsHide: true });
+    assert.equal(initialized.status, 0, initialized.stderr);
+    const old = path.join(dir, 'included-hooks');
+    writeText(path.join(old, 'pre-commit'), '#!/bin/sh\n# somebody else\n');
+    const included = path.join(dir, 'included.gitconfig');
+    writeText(included, `[core]\n hooksPath = ${JSON.stringify(old.replace(/\\/g, '/'))}\n`);
+    const heading = conditional
+      ? `[includeIf "gitdir:${fs.realpathSync(repo).replace(/\\/g, '/')}/"]`
+      : '[include]';
+    writeText(globalFile, `${heading}\n path = ${JSON.stringify(included.replace(/\\/g, '/'))}\n`);
+    assert.equal(hooksPath('global', gitPaths), old.replace(/\\/g, '/'), conditional ? 'conditional include at the real Git directory' : 'ordinary include');
+    const preview = installCommitGate({ kitHome: KIT_ROOT, env, gitPaths, cwd: repo, dryRun: true });
+    assert.equal(preview.previous, old.replace(/\\/g, '/'));
+    const installed = installCommitGate({ kitHome: KIT_ROOT, env, gitPaths, cwd: repo });
+    assert.equal(installed.ok, true);
+    assert.equal(installed.previous, old.replace(/\\/g, '/'));
+    assert.equal(previousHooksPath(gitPaths), old.replace(/\\/g, '/'));
+    const state = readJson(env.RESEARCH_KIT_INSTALL_STATE);
+    assert.equal(state.previousHooksPath, old.replace(/\\/g, '/'));
+    const removed = removeCommitGate({ env, gitPaths });
+    assert.equal(removed.restored, old.replace(/\\/g, '/'));
+    assert.equal(hooksPath('global', gitPaths), old.replace(/\\/g, '/'));
+  }
+});
+
 // A no-hit result describes inspected files. Reaching the count at the final file is
 // different from returning at that count while another path remains uninspected.
 test('secret cap: coverage distinguishes a complete boundary from an uninspected path', () => {