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/cli.test.ts

@@ -100,8 +100,10 @@ describe('parseCliArgs', () => {
     expect(result.maxBudget).toBe(15);
   });
 
-  it('throws on unknown options (strict mode)', () => {
-    expect(() => parseCliArgs(['--unknown-flag'])).toThrow();
+  it('ignores unknown options (non-strict for --pick support)', () => {
+    // strict: false allows --pick and other query-specific flags
+    const result = parseCliArgs(['--unknown-flag']);
+    expect(result.command).toBeUndefined();
   });
 
   // ─── Init command parsing ──────────────────────────────────────────────