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/query/config-query.test.ts

@@ -0,0 +1,161 @@
+/**
+ * Unit tests for config-get and resolve-model query handlers.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtemp, writeFile, mkdir, rm } from 'node:fs/promises';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { GSDError } from '../errors.js';
+
+// ─── Test setup ─────────────────────────────────────────────────────────────
+
+let tmpDir: string;
+
+beforeEach(async () => {
+  tmpDir = await mkdtemp(join(tmpdir(), 'gsd-cfg-'));
+  await mkdir(join(tmpDir, '.planning'), { recursive: true });
+});
+
+afterEach(async () => {
+  await rm(tmpDir, { recursive: true, force: true });
+});
+
+// ─── configGet ──────────────────────────────────────────────────────────────
+
+describe('configGet', () => {
+  it('returns raw config value for top-level key', async () => {
+    const { configGet } = await import('./config-query.js');
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ model_profile: 'quality' }),
+    );
+    const result = await configGet(['model_profile'], tmpDir);
+    expect(result.data).toBe('quality');
+  });
+
+  it('traverses dot-notation for nested keys', async () => {
+    const { configGet } = await import('./config-query.js');
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ workflow: { auto_advance: true } }),
+    );
+    const result = await configGet(['workflow.auto_advance'], tmpDir);
+    expect(result.data).toBe(true);
+  });
+
+  it('throws GSDError when no key provided', async () => {
+    const { configGet } = await import('./config-query.js');
+    await expect(configGet([], tmpDir)).rejects.toThrow(GSDError);
+  });
+
+  it('throws GSDError for nonexistent key', async () => {
+    const { configGet } = await import('./config-query.js');
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ model_profile: 'quality' }),
+    );
+    await expect(configGet(['nonexistent.key'], tmpDir)).rejects.toThrow(GSDError);
+  });
+
+  it('reads raw config without merging defaults', async () => {
+    const { configGet } = await import('./config-query.js');
+    // Write config with only model_profile -- no workflow section
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ model_profile: 'balanced' }),
+    );
+    // Accessing workflow should fail (not merged with defaults)
+    await expect(configGet(['workflow.auto_advance'], tmpDir)).rejects.toThrow(GSDError);
+  });
+});
+
+// ─── resolveModel ───────────────────────────────────────────────────────────
+
+describe('resolveModel', () => {
+  it('returns model and profile for known agent', async () => {
+    const { resolveModel } = await import('./config-query.js');
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ model_profile: 'balanced' }),
+    );
+    const result = await resolveModel(['gsd-planner'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data).toHaveProperty('model');
+    expect(data).toHaveProperty('profile', 'balanced');
+    expect(data).not.toHaveProperty('unknown_agent');
+  });
+
+  it('returns unknown_agent flag for unknown agent', async () => {
+    const { resolveModel } = await import('./config-query.js');
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ model_profile: 'balanced' }),
+    );
+    const result = await resolveModel(['unknown-agent'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data).toHaveProperty('model', 'sonnet');
+    expect(data).toHaveProperty('unknown_agent', true);
+  });
+
+  it('throws GSDError when no agent type provided', async () => {
+    const { resolveModel } = await import('./config-query.js');
+    await expect(resolveModel([], tmpDir)).rejects.toThrow(GSDError);
+  });
+
+  it('respects model_overrides from config', async () => {
+    const { resolveModel } = await import('./config-query.js');
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({
+        model_profile: 'balanced',
+        model_overrides: { 'gsd-planner': 'openai/gpt-5.4' },
+      }),
+    );
+    const result = await resolveModel(['gsd-planner'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data).toHaveProperty('model', 'openai/gpt-5.4');
+  });
+
+  it('returns empty model when resolve_model_ids is omit', async () => {
+    const { resolveModel } = await import('./config-query.js');
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({
+        model_profile: 'balanced',
+        resolve_model_ids: 'omit',
+      }),
+    );
+    const result = await resolveModel(['gsd-planner'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data).toHaveProperty('model', '');
+  });
+});
+
+// ─── MODEL_PROFILES ─────────────────────────────────────────────────────────
+
+describe('MODEL_PROFILES', () => {
+  it('contains all 17 agent entries', async () => {
+    const { MODEL_PROFILES } = await import('./config-query.js');
+    expect(Object.keys(MODEL_PROFILES)).toHaveLength(17);
+  });
+
+  it('has quality/balanced/budget/adaptive for each agent', async () => {
+    const { MODEL_PROFILES } = await import('./config-query.js');
+    for (const agent of Object.keys(MODEL_PROFILES)) {
+      expect(MODEL_PROFILES[agent]).toHaveProperty('quality');
+      expect(MODEL_PROFILES[agent]).toHaveProperty('balanced');
+      expect(MODEL_PROFILES[agent]).toHaveProperty('budget');
+      expect(MODEL_PROFILES[agent]).toHaveProperty('adaptive');
+    }
+  });
+});
+
+// ─── VALID_PROFILES ─────────────────────────────────────────────────────────
+
+describe('VALID_PROFILES', () => {
+  it('contains the four profile names', async () => {
+    const { VALID_PROFILES } = await import('./config-query.js');
+    expect(VALID_PROFILES).toEqual(['quality', 'balanced', 'budget', 'adaptive']);
+  });
+});