test: add test isolation and pause wiring tests

- worktree.ts: Added _resetServiceCache() for test isolation
- test-isolation.ts: Shared test isolation utilities
- 5 worktree tests: Isolate from global ~/.gsd/preferences.md
- 2 RTK tests: Clear GSD_RTK_DISABLED before running
- pre-execution-pause-wiring.test.ts: Pause wiring integration tests
- preferences.ts: Add enhanced_verification to mergePreferences

src/resources/extensions/gsd/tests/integration/test-isolation.ts

@@ -0,0 +1,53 @@
+/**
+ * Test isolation utilities for integration tests.
+ *
+ * Integration tests often call `mergeMilestoneToMain` and other functions that
+ * load preferences. If the user's global ~/.gsd/preferences.md has
+ * `git.main_branch: master`, tests fail because test repos use `main`.
+ *
+ * These utilities isolate tests from the user's global environment.
+ */
+
+import { mkdtempSync, rmSync, realpathSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { _resetServiceCache } from "../../worktree.ts";
+import { _clearGsdRootCache } from "../../paths.ts";
+
+let originalHome: string | undefined;
+let fakeHome: string | null = null;
+
+/**
+ * Isolate the test environment from user's global preferences.
+ * Creates a fake HOME directory so loadEffectiveGSDPreferences() returns
+ * empty global preferences instead of the user's ~/.gsd/preferences.md.
+ *
+ * Call this in a test.before() hook.
+ */
+export function isolateFromGlobalPreferences(): void {
+  originalHome = process.env.HOME;
+  fakeHome = realpathSync(mkdtempSync(join(tmpdir(), "gsd-test-home-")));
+  process.env.HOME = fakeHome;
+  _clearGsdRootCache();
+  _resetServiceCache();
+}
+
+/**
+ * Restore the original HOME and clean up the fake home directory.
+ *
+ * Call this in a test.after() hook.
+ */
+export function restoreGlobalPreferences(): void {
+  if (originalHome !== undefined) {
+    process.env.HOME = originalHome;
+  } else {
+    delete process.env.HOME;
+  }
+  _clearGsdRootCache();
+  _resetServiceCache();
+  if (fakeHome) {
+    rmSync(fakeHome, { recursive: true, force: true });
+    fakeHome = null;
+  }
+}

src/resources/extensions/gsd/tests/stale-worktree-cwd.test.ts

@@ -17,6 +17,8 @@ import {
   teardownAutoWorktree,
   mergeMilestoneToMain,
 } from "../auto-worktree.ts";
+import { _resetServiceCache } from "../worktree.ts";
+import { _clearGsdRootCache } from "../paths.ts";
 
 function run(command: string, cwd: string): string {
   return execSync(command, { cwd, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" }).trim();
@@ -62,6 +64,13 @@ test("mergeMilestoneToMain restores cwd to project root", () => {
   const savedCwd = process.cwd();
   let tempDir = "";
 
+  // Isolate from user's global preferences (which may have git.main_branch set)
+  const originalHome = process.env.HOME;
+  const fakeHome = realpathSync(mkdtempSync(join(tmpdir(), "gsd-fake-home-")));
+  process.env.HOME = fakeHome;
+  _clearGsdRootCache();
+  _resetServiceCache();
+
   try {
     tempDir = createTempRepo();
 
@@ -97,9 +106,13 @@ test("mergeMilestoneToMain restores cwd to project root", () => {
     assert.ok(!existsSync(wtPath), "worktree directory removed after merge");
   } finally {
     process.chdir(savedCwd);
+    process.env.HOME = originalHome;
+    _clearGsdRootCache();
+    _resetServiceCache();
     if (tempDir && existsSync(tempDir)) {
       rmSync(tempDir, { recursive: true, force: true });
     }
+    rmSync(fakeHome, { recursive: true, force: true });
   }
 });
 

src/resources/extensions/gsd/tests/stash-pop-gsd-conflict.test.ts

@@ -15,6 +15,27 @@ import { tmpdir } from "node:os";
 import { execSync } from "node:child_process";
 
 import { createAutoWorktree, mergeMilestoneToMain } from "../auto-worktree.ts";
+import { _resetServiceCache } from "../worktree.ts";
+import { _clearGsdRootCache } from "../paths.ts";
+
+// Isolate from user's global preferences (which may have git.main_branch set)
+let originalHome: string | undefined;
+let fakeHome: string;
+
+test.before(() => {
+  originalHome = process.env.HOME;
+  fakeHome = realpathSync(mkdtempSync(join(tmpdir(), "gsd-fake-home-")));
+  process.env.HOME = fakeHome;
+  _clearGsdRootCache();
+  _resetServiceCache();
+});
+
+test.after(() => {
+  process.env.HOME = originalHome;
+  _clearGsdRootCache();
+  _resetServiceCache();
+  rmSync(fakeHome, { recursive: true, force: true });
+});
 
 function run(cmd: string, cwd: string): string {
   return execSync(cmd, { cwd, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" }).trim();

src/resources/extensions/gsd/tests/stash-queued-context-files.test.ts

@@ -27,6 +27,27 @@ import { tmpdir } from "node:os";
 import { execSync } from "node:child_process";
 
 import { createAutoWorktree, mergeMilestoneToMain } from "../auto-worktree.ts";
+import { _resetServiceCache } from "../worktree.ts";
+import { _clearGsdRootCache } from "../paths.ts";
+
+// Isolate from user's global preferences (which may have git.main_branch set)
+let originalHome: string | undefined;
+let fakeHome: string;
+
+test.before(() => {
+  originalHome = process.env.HOME;
+  fakeHome = realpathSync(mkdtempSync(join(tmpdir(), "gsd-fake-home-")));
+  process.env.HOME = fakeHome;
+  _clearGsdRootCache();
+  _resetServiceCache();
+});
+
+test.after(() => {
+  process.env.HOME = originalHome;
+  _clearGsdRootCache();
+  _resetServiceCache();
+  rmSync(fakeHome, { recursive: true, force: true });
+});
 
 function run(cmd: string, cwd: string): string {
   return execSync(cmd, {

src/resources/extensions/gsd/tests/worktree-integration.test.ts

@@ -26,9 +26,11 @@ import {
   getSliceBranchName,
   autoCommitCurrentBranch,
   SLICE_BRANCH_RE,
+  _resetServiceCache,
 } from "../worktree.ts";
 
 import { deriveState } from "../state.ts";
+import { _clearGsdRootCache } from "../paths.ts";
 import { describe, test } from 'node:test';
 import assert from 'node:assert/strict';
 
@@ -74,6 +76,14 @@ run("git add .", base);
 run('git commit -m "chore: init"', base);
 
 describe('worktree-integration', async () => {
+  // Isolate from user's global preferences (which may have git.main_branch set).
+  // Reset caches so getService() creates a fresh instance with empty preferences.
+  const originalHome = process.env.HOME;
+  const fakeHome = mkdtempSync(join(tmpdir(), "gsd-fake-home-"));
+  process.env.HOME = fakeHome;
+  _clearGsdRootCache();
+  _resetServiceCache();
+
   // ── Verify main tree baseline ──────────────────────────────────────────────
 
   console.log("\n=== Main tree baseline ===");
@@ -197,4 +207,10 @@ describe('worktree-integration', async () => {
   assert.deepStrictEqual(listWorktrees(base).length, 0, "all worktrees removed");
 
   rmSync(base, { recursive: true, force: true });
+
+  // Restore HOME and reset caches
+  process.env.HOME = originalHome;
+  _clearGsdRootCache();
+  _resetServiceCache();
+  rmSync(fakeHome, { recursive: true, force: true });
 });

src/resources/extensions/gsd/tests/worktree.test.ts

@@ -14,9 +14,11 @@ import {
   resolveProjectRoot,
   setActiveMilestoneId,
   SLICE_BRANCH_RE,
+  _resetServiceCache,
 } from "../worktree.ts";
 import { readIntegrationBranch } from "../git-service.ts";
 import { _resetHasChangesCache } from "../native-git-bridge.ts";
+import { _clearGsdRootCache } from "../paths.ts";
 import { describe, test } from 'node:test';
 import assert from 'node:assert/strict';
 
@@ -165,15 +167,30 @@ describe('worktree', async () => {
     run("git checkout -b my-feature", repo);
     captureIntegrationBranch(repo, "M001");
 
-    // Without milestone set, getMainBranch returns "main"
-    setActiveMilestoneId(repo, null);
-    assert.deepStrictEqual(getMainBranch(repo), "main",
-      "getMainBranch returns main without milestone set");
+    // Isolate from user's global preferences (which may have git.main_branch set).
+    // Reset caches so getService() creates a fresh instance with empty preferences.
+    const originalHome = process.env.HOME;
+    const fakeHome = mkdtempSync(join(tmpdir(), "gsd-fake-home-"));
+    process.env.HOME = fakeHome;
+    _clearGsdRootCache();
+    _resetServiceCache();
 
-    // With milestone set, getMainBranch returns feature branch
-    setActiveMilestoneId(repo, "M001");
-    assert.deepStrictEqual(getMainBranch(repo), "my-feature",
-      "getMainBranch returns integration branch with milestone set");
+    try {
+      // Without milestone set, getMainBranch returns "main"
+      setActiveMilestoneId(repo, null);
+      assert.deepStrictEqual(getMainBranch(repo), "main",
+        "getMainBranch returns main without milestone set");
+
+      // With milestone set, getMainBranch returns feature branch
+      setActiveMilestoneId(repo, "M001");
+      assert.deepStrictEqual(getMainBranch(repo), "my-feature",
+        "getMainBranch returns integration branch with milestone set");
+    } finally {
+      process.env.HOME = originalHome;
+      _clearGsdRootCache();
+      _resetServiceCache();
+      rmSync(fakeHome, { recursive: true, force: true });
+    }
 
     rmSync(repo, { recursive: true, force: true });
   }

src/resources/extensions/gsd/worktree.ts

@@ -42,6 +42,16 @@ function getService(basePath: string): GitServiceImpl {
   return cachedService;
 }
 
+/**
+ * Clear the cached GitServiceImpl. For testing only — forces the next
+ * getService() call to re-read preferences and create a fresh instance.
+ * @internal
+ */
+export function _resetServiceCache(): void {
+  cachedService = null;
+  cachedBasePath = null;
+}
+
 /**
  * Set the active milestone ID on the cached GitServiceImpl.
  * This enables integration branch resolution in getMainBranch().

src/tests/rtk-session-stats.test.ts

@@ -1,4 +1,4 @@
-import test from "node:test";
+import test, { beforeEach, afterEach } from "node:test";
 import assert from "node:assert/strict";
 import { chmodSync, copyFileSync, mkdirSync, mkdtempSync, rmSync } from "node:fs";
 import { join } from "node:path";
@@ -12,6 +12,24 @@ import {
 } from "../resources/extensions/shared/rtk-session-stats.ts";
 import { createFakeRtk } from "./rtk-test-utils.ts";
 
+// Store original env values for restoration
+let originalRtkDisabled: string | undefined;
+
+beforeEach(() => {
+  // Save and clear GSD_RTK_DISABLED so tests can use fake RTK binaries
+  originalRtkDisabled = process.env.GSD_RTK_DISABLED;
+  delete process.env.GSD_RTK_DISABLED;
+});
+
+afterEach(() => {
+  // Restore original env
+  if (originalRtkDisabled !== undefined) {
+    process.env.GSD_RTK_DISABLED = originalRtkDisabled;
+  } else {
+    delete process.env.GSD_RTK_DISABLED;
+  }
+});
+
 function summary(totalCommands: number, totalInput: number, totalOutput: number, totalSaved: number, totalTimeMs = 1000) {
   return JSON.stringify({
     summary: {

src/tests/rtk.test.ts

@@ -1,4 +1,4 @@
-import test from "node:test";
+import test, { beforeEach, afterEach } from "node:test";
 import assert from "node:assert/strict";
 import { chmodSync, copyFileSync, mkdirSync, mkdtempSync, rmSync } from "node:fs";
 import { tmpdir } from "node:os";
@@ -19,6 +19,24 @@ import {
 } from "../rtk.ts";
 import { createFakeRtk } from "./rtk-test-utils.ts";
 
+// Store original env values for restoration
+let originalRtkDisabled: string | undefined;
+
+beforeEach(() => {
+  // Save and clear GSD_RTK_DISABLED so tests can use fake RTK binaries
+  originalRtkDisabled = process.env.GSD_RTK_DISABLED;
+  delete process.env.GSD_RTK_DISABLED;
+});
+
+afterEach(() => {
+  // Restore original env
+  if (originalRtkDisabled !== undefined) {
+    process.env.GSD_RTK_DISABLED = originalRtkDisabled;
+  } else {
+    delete process.env.GSD_RTK_DISABLED;
+  }
+});
+
 test("resolveRtkAssetName maps supported release assets correctly", () => {
   assert.equal(resolveRtkAssetName("darwin", "arm64"), "rtk-aarch64-apple-darwin.tar.gz");
   assert.equal(resolveRtkAssetName("darwin", "x64"), "rtk-x86_64-apple-darwin.tar.gz");