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/context-engine.ts

@@ -64,6 +64,11 @@ const PHASE_FILE_MANIFEST: Record<PhaseType, FileSpec[]> = {
     { key: 'plan', filename: 'PLAN.md', required: false },
     { key: 'summary', filename: 'SUMMARY.md', required: false },
   ],
+  [PhaseType.Repair]: [
+    { key: 'state', filename: 'STATE.md', required: true },
+    { key: 'config', filename: 'config.json', required: false },
+    { key: 'plan', filename: 'PLAN.md', required: false },
+  ],
   [PhaseType.Discuss]: [
     { key: 'state', filename: 'STATE.md', required: true },
     { key: 'roadmap', filename: 'ROADMAP.md', required: false },