fix(2137): skip worktree isolation when .gitmodules detected (#2144)

* feat(sdk): add typed query foundation and gsd-sdk query (Phase 1)

Add sdk/src/query registry and handlers with tests, GSDQueryError, CLI query wiring, and supporting type/tool-scoping hooks. Update CHANGELOG. Vitest 4 constructor mock fixes in milestone-runner tests.

Made-with: Cursor

* fix(2137): skip worktree isolation when .gitmodules detected

When a project contains git submodules, worktree isolation cannot
correctly handle submodule commits — three separate gaps exist in
worktree setup, executor commit protocol, and merge-back. Rather
than patch each gap individually, detect .gitmodules at phase start
and fall back to sequential execution, which handles submodules
transparently (Option B).

Affected workflows: execute-phase.md, quick.md

---------

Co-authored-by: David Sienkowski <dave@sienkowski.com>

sdk/src/milestone-runner.test.ts

@@ -36,12 +36,15 @@ vi.mock('./prompt-builder.js', () => ({
 
 vi.mock('./event-stream.js', () => {
   return {
-    GSDEventStream: vi.fn().mockImplementation(() => ({
-      emitEvent: vi.fn(),
-      on: vi.fn(),
-      emit: vi.fn(),
-      addTransport: vi.fn(),
-    })),
+    // Use function (not arrow) so `new GSDEventStream()` works under Vitest 4
+    GSDEventStream: vi.fn(function GSDEventStreamMock() {
+      return {
+        emitEvent: vi.fn(),
+        on: vi.fn(),
+        emit: vi.fn(),
+        addTransport: vi.fn(),
+      };
+    }),
   };
 });
 
@@ -65,9 +68,12 @@ vi.mock('./phase-prompt.js', () => ({
 }));
 
 vi.mock('./gsd-tools.js', () => ({
-  GSDTools: vi.fn().mockImplementation(() => ({
-    roadmapAnalyze: vi.fn(),
-  })),
+  // Constructor mock for `new GSDTools(...)` (Vitest 4)
+  GSDTools: vi.fn(function GSDToolsMock() {
+    return {
+      roadmapAnalyze: vi.fn(),
+    };
+  }),
   GSDToolsError: class extends Error {
     name = 'GSDToolsError';
   },
@@ -125,12 +131,11 @@ describe('GSD.run()', () => {
 
     // Wire mock roadmapAnalyze on the GSDTools instance
     mockRoadmapAnalyze = vi.fn();
-    vi.mocked(GSDTools).mockImplementation(
-      () =>
-        ({
-          roadmapAnalyze: mockRoadmapAnalyze,
-        }) as any,
-    );
+    vi.mocked(GSDTools).mockImplementation(function () {
+      return {
+        roadmapAnalyze: mockRoadmapAnalyze,
+      } as any;
+    });
   });
 
   it('discovers phases and calls runPhase for each incomplete one', async () => {