fix(hooks): include configured hooks in scoped reads

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`,

research-kit/README.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/lib/machine.mjs

@@ -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/test/doctor.test.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 +26,43 @@ 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 = ${JSON.stringify(old.replace(/\\/g, '/'))}\n`);
+    const gitTopLevel = spawnSync('git', ['rev-parse', '--show-toplevel'], {
+      cwd: repo, env: gitPaths.env, encoding: 'utf8', windowsHide: true,
+    });
+    assert.equal(gitTopLevel.status, 0, gitTopLevel.stderr);
+    const heading = conditional
+      ? `[includeIf "gitdir:${gitTopLevel.stdout.trim().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 Git’s resolved worktree path' : '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', () => {