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>
2026-04-12 08:33:04 -04:00
parent 58632e0718
commit 002bcf2a8a
63 changed files with 17872 additions and 23 deletions
--- a/sdk/src/query/validate.test.ts
+++ b/sdk/src/query/validate.test.ts
@@ -0,0 +1,642 @@
+/**
+ * Tests for validation query handlers — verifyKeyLinks, validateConsistency, validateHealth.
+ *
+ * Uses temp directories with fixture files to test verification logic.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtemp, writeFile, mkdir, rm, readFile } from 'node:fs/promises';
+import { join } from 'node:path';
+import { tmpdir, homedir } from 'node:os';
+import { GSDError } from '../errors.js';
+
+import { verifyKeyLinks, validateConsistency, validateHealth } from './validate.js';
+
+// ─── verifyKeyLinks ────────────────────────────────────────────────────────
+
+describe('verifyKeyLinks', () => {
+  let tmpDir: string;
+
+  beforeEach(async () => {
+    tmpDir = await mkdtemp(join(tmpdir(), 'gsd-validate-'));
+  });
+
+  afterEach(async () => {
+    await rm(tmpDir, { recursive: true, force: true });
+  });
+
+  it('throws GSDError Validation when no args', async () => {
+    let caught: unknown;
+    try {
+      await verifyKeyLinks([], tmpDir);
+    } catch (err) {
+      caught = err;
+    }
+    expect(caught).toBeInstanceOf(GSDError);
+    expect((caught as GSDError).classification).toBe('validation');
+  });
+
+  it('returns all_verified true when pattern found in source', async () => {
+    // Create source file with an import statement
+    await writeFile(join(tmpDir, 'source.ts'), "import { foo } from './target.js';");
+    await writeFile(join(tmpDir, 'target.ts'), 'export const foo = 1;');
+
+    // Create plan with key_links
+    const planContent = `---
+phase: 01
+plan: 01
+type: execute
+wave: 1
+depends_on: []
+files_modified: []
+autonomous: true
+
+must_haves:
+  key_links:
+    - from: source.ts
+      to: target.ts
+      via: "import foo"
+      pattern: "import.*foo.*from.*target"
+---
+
+# Plan
+`;
+    await writeFile(join(tmpDir, 'plan.md'), planContent);
+
+    const result = await verifyKeyLinks(['plan.md'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.all_verified).toBe(true);
+    expect(data.verified).toBe(1);
+    expect(data.total).toBe(1);
+    const links = data.links as Array<Record<string, unknown>>;
+    expect(links[0].detail).toBe('Pattern found in source');
+  });
+
+  it('returns verified true with "Pattern found in target" when not in source but in target', async () => {
+    await writeFile(join(tmpDir, 'source.ts'), 'const x = 1;');
+    await writeFile(join(tmpDir, 'target.ts'), "import { foo } from './other.js';");
+
+    const planContent = `---
+phase: 01
+plan: 01
+type: execute
+wave: 1
+depends_on: []
+files_modified: []
+autonomous: true
+
+must_haves:
+  key_links:
+    - from: source.ts
+      to: target.ts
+      via: "import foo"
+      pattern: "import.*foo"
+---
+
+# Plan
+`;
+    await writeFile(join(tmpDir, 'plan.md'), planContent);
+
+    const result = await verifyKeyLinks(['plan.md'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const links = data.links as Array<Record<string, unknown>>;
+    expect(links[0].verified).toBe(true);
+    expect(links[0].detail).toBe('Pattern found in target');
+  });
+
+  it('returns verified false when pattern not found in source or target', async () => {
+    await writeFile(join(tmpDir, 'source.ts'), 'const x = 1;');
+    await writeFile(join(tmpDir, 'target.ts'), 'const y = 2;');
+
+    const planContent = `---
+phase: 01
+plan: 01
+type: execute
+wave: 1
+depends_on: []
+files_modified: []
+autonomous: true
+
+must_haves:
+  key_links:
+    - from: source.ts
+      to: target.ts
+      via: "import foo"
+      pattern: "import.*foo"
+---
+
+# Plan
+`;
+    await writeFile(join(tmpDir, 'plan.md'), planContent);
+
+    const result = await verifyKeyLinks(['plan.md'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.all_verified).toBe(false);
+    const links = data.links as Array<Record<string, unknown>>;
+    expect(links[0].verified).toBe(false);
+  });
+
+  it('returns Source file not found when source missing', async () => {
+    await writeFile(join(tmpDir, 'target.ts'), 'export const foo = 1;');
+
+    const planContent = `---
+phase: 01
+plan: 01
+type: execute
+wave: 1
+depends_on: []
+files_modified: []
+autonomous: true
+
+must_haves:
+  key_links:
+    - from: missing.ts
+      to: target.ts
+      via: "import"
+      pattern: "import"
+---
+
+# Plan
+`;
+    await writeFile(join(tmpDir, 'plan.md'), planContent);
+
+    const result = await verifyKeyLinks(['plan.md'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const links = data.links as Array<Record<string, unknown>>;
+    expect(links[0].detail).toBe('Source file not found');
+    expect(links[0].verified).toBe(false);
+  });
+
+  it('checks target reference in source when no pattern specified', async () => {
+    await writeFile(join(tmpDir, 'source.ts'), "import { foo } from './target.ts';");
+    await writeFile(join(tmpDir, 'target.ts'), 'export const foo = 1;');
+
+    const planContent = `---
+phase: 01
+plan: 01
+type: execute
+wave: 1
+depends_on: []
+files_modified: []
+autonomous: true
+
+must_haves:
+  key_links:
+    - from: source.ts
+      to: target.ts
+      via: "import"
+---
+
+# Plan
+`;
+    await writeFile(join(tmpDir, 'plan.md'), planContent);
+
+    const result = await verifyKeyLinks(['plan.md'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const links = data.links as Array<Record<string, unknown>>;
+    expect(links[0].verified).toBe(true);
+    expect(links[0].detail).toBe('Target referenced in source');
+  });
+
+  it('returns Invalid regex pattern for bad regex', async () => {
+    await writeFile(join(tmpDir, 'source.ts'), 'const x = 1;');
+    await writeFile(join(tmpDir, 'target.ts'), 'const y = 2;');
+
+    const planContent = `---
+phase: 01
+plan: 01
+type: execute
+wave: 1
+depends_on: []
+files_modified: []
+autonomous: true
+
+must_haves:
+  key_links:
+    - from: source.ts
+      to: target.ts
+      via: "bad regex"
+      pattern: "[invalid"
+---
+
+# Plan
+`;
+    await writeFile(join(tmpDir, 'plan.md'), planContent);
+
+    const result = await verifyKeyLinks(['plan.md'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const links = data.links as Array<Record<string, unknown>>;
+    expect(links[0].verified).toBe(false);
+    expect((links[0].detail as string).startsWith('Invalid regex pattern')).toBe(true);
+  });
+
+  it('returns error when no must_haves.key_links in plan', async () => {
+    const planContent = `---
+phase: 01
+plan: 01
+type: execute
+wave: 1
+depends_on: []
+files_modified: []
+autonomous: true
+---
+
+# Plan
+`;
+    await writeFile(join(tmpDir, 'plan.md'), planContent);
+
+    const result = await verifyKeyLinks(['plan.md'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.error).toBe('No must_haves.key_links found in frontmatter');
+  });
+});
+
+// ─── validateConsistency ──────────────────────────────────────────────────
+
+describe('validateConsistency', () => {
+  let tmpDir: string;
+
+  beforeEach(async () => {
+    tmpDir = await mkdtemp(join(tmpdir(), 'gsd-consistency-'));
+  });
+
+  afterEach(async () => {
+    await rm(tmpDir, { recursive: true, force: true });
+  });
+
+  /** Helper: create a .planning directory structure */
+  async function createPlanning(opts: {
+    roadmap?: string;
+    phases?: Array<{ dir: string; plans?: string[]; summaries?: string[]; planContents?: Record<string, string> }>;
+    config?: Record<string, unknown>;
+  }): Promise<void> {
+    const planning = join(tmpDir, '.planning');
+    await mkdir(planning, { recursive: true });
+
+    if (opts.roadmap !== undefined) {
+      await writeFile(join(planning, 'ROADMAP.md'), opts.roadmap);
+    }
+
+    if (opts.config) {
+      await writeFile(join(planning, 'config.json'), JSON.stringify(opts.config));
+    }
+
+    if (opts.phases) {
+      const phasesDir = join(planning, 'phases');
+      await mkdir(phasesDir, { recursive: true });
+      for (const phase of opts.phases) {
+        const phaseDir = join(phasesDir, phase.dir);
+        await mkdir(phaseDir, { recursive: true });
+        if (phase.plans) {
+          for (const plan of phase.plans) {
+            const content = phase.planContents?.[plan] ?? `---\nphase: ${phase.dir}\nplan: 01\ntype: execute\nwave: 1\ndepends_on: []\nfiles_modified: []\nautonomous: true\n---\n\n# Plan\n`;
+            await writeFile(join(phaseDir, plan), content);
+          }
+        }
+        if (phase.summaries) {
+          for (const summary of phase.summaries) {
+            await writeFile(join(phaseDir, summary), '# Summary\n');
+          }
+        }
+      }
+    }
+  }
+
+  it('returns passed true when ROADMAP phases match disk', async () => {
+    await createPlanning({
+      roadmap: '# Roadmap\n\n## Phase 1: Foundation\n\nGoal here.\n\n## Phase 2: Features\n\nMore goals.\n',
+      phases: [
+        { dir: '01-foundation', plans: ['01-01-PLAN.md'], summaries: ['01-01-SUMMARY.md'] },
+        { dir: '02-features', plans: ['02-01-PLAN.md'], summaries: ['02-01-SUMMARY.md'] },
+      ],
+      config: { phase_naming: 'sequential' },
+    });
+
+    const result = await validateConsistency([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.passed).toBe(true);
+    expect((data.errors as string[]).length).toBe(0);
+    expect((data.warnings as string[]).length).toBe(0);
+  });
+
+  it('warns when phase in ROADMAP but not on disk', async () => {
+    await createPlanning({
+      roadmap: '# Roadmap\n\n## Phase 1: Foundation\n\n## Phase 2: Features\n\n## Phase 3: Polish\n',
+      phases: [
+        { dir: '01-foundation', plans: ['01-01-PLAN.md'] },
+        { dir: '02-features', plans: ['02-01-PLAN.md'] },
+      ],
+      config: { phase_naming: 'sequential' },
+    });
+
+    const result = await validateConsistency([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as string[];
+    expect(warnings.some(w => w.includes('Phase 3') && w.includes('ROADMAP') && w.includes('no directory'))).toBe(true);
+  });
+
+  it('warns when phase on disk but not in ROADMAP', async () => {
+    await createPlanning({
+      roadmap: '# Roadmap\n\n## Phase 1: Foundation\n',
+      phases: [
+        { dir: '01-foundation', plans: ['01-01-PLAN.md'] },
+        { dir: '02-features', plans: ['02-01-PLAN.md'] },
+      ],
+      config: { phase_naming: 'sequential' },
+    });
+
+    const result = await validateConsistency([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as string[];
+    expect(warnings.some(w => w.includes('02') && w.includes('disk') && w.includes('not in ROADMAP'))).toBe(true);
+  });
+
+  it('warns on gap in sequential phase numbering', async () => {
+    await createPlanning({
+      roadmap: '# Roadmap\n\n## Phase 1: Foundation\n\n## Phase 3: Polish\n',
+      phases: [
+        { dir: '01-foundation', plans: ['01-01-PLAN.md'] },
+        { dir: '03-polish', plans: ['03-01-PLAN.md'] },
+      ],
+      config: { phase_naming: 'sequential' },
+    });
+
+    const result = await validateConsistency([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as string[];
+    expect(warnings.some(w => w.includes('Gap in phase numbering'))).toBe(true);
+  });
+
+  it('warns on plan numbering gap within phase', async () => {
+    await createPlanning({
+      roadmap: '# Roadmap\n\n## Phase 1: Foundation\n',
+      phases: [
+        { dir: '01-foundation', plans: ['01-01-PLAN.md', '01-03-PLAN.md'] },
+      ],
+      config: { phase_naming: 'sequential' },
+    });
+
+    const result = await validateConsistency([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as string[];
+    expect(warnings.some(w => w.includes('Gap in plan numbering'))).toBe(true);
+  });
+
+  it('warns on summary without matching plan', async () => {
+    await createPlanning({
+      roadmap: '# Roadmap\n\n## Phase 1: Foundation\n',
+      phases: [
+        { dir: '01-foundation', plans: ['01-01-PLAN.md'], summaries: ['01-01-SUMMARY.md', '01-02-SUMMARY.md'] },
+      ],
+      config: { phase_naming: 'sequential' },
+    });
+
+    const result = await validateConsistency([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as string[];
+    expect(warnings.some(w => w.includes('Summary') && w.includes('no matching PLAN'))).toBe(true);
+  });
+
+  it('warns when plan missing wave in frontmatter', async () => {
+    const noWavePlan = `---\nphase: 01\nplan: 01\ntype: execute\ndepends_on: []\nfiles_modified: []\nautonomous: true\n---\n\n# Plan\n`;
+    await createPlanning({
+      roadmap: '# Roadmap\n\n## Phase 1: Foundation\n',
+      phases: [
+        { dir: '01-foundation', plans: ['01-01-PLAN.md'], planContents: { '01-01-PLAN.md': noWavePlan } },
+      ],
+      config: { phase_naming: 'sequential' },
+    });
+
+    const result = await validateConsistency([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as string[];
+    expect(warnings.some(w => w.includes('wave') && w.includes('frontmatter'))).toBe(true);
+  });
+
+  it('returns passed false with error when ROADMAP.md missing', async () => {
+    await createPlanning({
+      phases: [{ dir: '01-foundation', plans: ['01-01-PLAN.md'] }],
+      config: { phase_naming: 'sequential' },
+    });
+
+    const result = await validateConsistency([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.passed).toBe(false);
+    expect((data.errors as string[])).toContain('ROADMAP.md not found');
+  });
+});
+
+// ─── validateHealth ─────────────────────────────────────────────────────────
+
+describe('validateHealth', () => {
+  let tmpDir: string;
+
+  beforeEach(async () => {
+    tmpDir = await mkdtemp(join(tmpdir(), 'gsd-health-'));
+  });
+
+  afterEach(async () => {
+    await rm(tmpDir, { recursive: true, force: true });
+  });
+
+  /** Helper: create a healthy .planning directory structure */
+  async function createHealthyPlanning(): Promise<void> {
+    const planning = join(tmpDir, '.planning');
+    await mkdir(join(planning, 'phases', '01-foundation'), { recursive: true });
+
+    await writeFile(join(planning, 'PROJECT.md'), '# Project\n\n## What This Is\n\nA project.\n\n## Core Value\n\nValue here.\n\n## Requirements\n\n- Req 1\n');
+    await writeFile(join(planning, 'ROADMAP.md'), '# Roadmap\n\n## Phase 1: Foundation\n\nGoals.\n');
+    await writeFile(join(planning, 'STATE.md'), '---\nstatus: executing\n---\n\n# State\n\n**Current Phase:** 1\n**Status:** executing\n');
+    await writeFile(join(planning, 'config.json'), JSON.stringify({
+      model_profile: 'balanced',
+      workflow: { nyquist_validation: true },
+    }, null, 2));
+
+    await writeFile(join(planning, 'phases', '01-foundation', '01-01-PLAN.md'), '---\nphase: 01\nplan: 01\ntype: execute\nwave: 1\ndepends_on: []\nfiles_modified: []\nautonomous: true\n---\n\n# Plan\n');
+    await writeFile(join(planning, 'phases', '01-foundation', '01-01-SUMMARY.md'), '# Summary\n');
+  }
+
+  it('returns healthy status when all files present', async () => {
+    await createHealthyPlanning();
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.status).toBe('healthy');
+    expect((data.errors as unknown[]).length).toBe(0);
+    expect((data.warnings as unknown[]).length).toBe(0);
+  });
+
+  it('returns broken with E001 when no .planning/ directory', async () => {
+    // tmpDir has no .planning/ — already the case
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.status).toBe('broken');
+    const errors = data.errors as Array<Record<string, unknown>>;
+    expect(errors.some(e => e.code === 'E001')).toBe(true);
+  });
+
+  it('returns error E002 when PROJECT.md missing', async () => {
+    await createHealthyPlanning();
+    const { unlink } = await import('node:fs/promises');
+    await unlink(join(tmpDir, '.planning', 'PROJECT.md'));
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const errors = data.errors as Array<Record<string, unknown>>;
+    expect(errors.some(e => e.code === 'E002')).toBe(true);
+  });
+
+  it('returns error E003 when ROADMAP.md missing', async () => {
+    await createHealthyPlanning();
+    const { unlink } = await import('node:fs/promises');
+    await unlink(join(tmpDir, '.planning', 'ROADMAP.md'));
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const errors = data.errors as Array<Record<string, unknown>>;
+    expect(errors.some(e => e.code === 'E003')).toBe(true);
+  });
+
+  it('returns error E004 when STATE.md missing (repairable)', async () => {
+    await createHealthyPlanning();
+    const { unlink } = await import('node:fs/promises');
+    await unlink(join(tmpDir, '.planning', 'STATE.md'));
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const errors = data.errors as Array<Record<string, unknown>>;
+    const e004 = errors.find(e => e.code === 'E004');
+    expect(e004).toBeDefined();
+    expect(e004!.repairable).toBe(true);
+  });
+
+  it('returns error E005 when config.json has invalid JSON (repairable)', async () => {
+    await createHealthyPlanning();
+    await writeFile(join(tmpDir, '.planning', 'config.json'), '{invalid json!!!');
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const errors = data.errors as Array<Record<string, unknown>>;
+    const e005 = errors.find(e => e.code === 'E005');
+    expect(e005).toBeDefined();
+    expect(e005!.repairable).toBe(true);
+  });
+
+  it('returns warning W003 when config.json missing (repairable)', async () => {
+    await createHealthyPlanning();
+    const { unlink } = await import('node:fs/promises');
+    await unlink(join(tmpDir, '.planning', 'config.json'));
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as Array<Record<string, unknown>>;
+    const w003 = warnings.find(w => w.code === 'W003');
+    expect(w003).toBeDefined();
+    expect(w003!.repairable).toBe(true);
+  });
+
+  it('returns warning W005 for bad phase directory naming', async () => {
+    await createHealthyPlanning();
+    await mkdir(join(tmpDir, '.planning', 'phases', 'bad_name'), { recursive: true });
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as Array<Record<string, unknown>>;
+    expect(warnings.some(w => w.code === 'W005')).toBe(true);
+  });
+
+  it('returns early with E010 when CWD equals home directory', async () => {
+    const result = await validateHealth([], homedir());
+    const data = result.data as Record<string, unknown>;
+    expect(data.status).toBe('error');
+    const errors = data.errors as Array<Record<string, unknown>>;
+    expect(errors.some(e => e.code === 'E010')).toBe(true);
+  });
+
+  it('returns warning W008 when config.json missing workflow.nyquist_validation', async () => {
+    await createHealthyPlanning();
+    await writeFile(join(tmpDir, '.planning', 'config.json'), JSON.stringify({
+      model_profile: 'balanced',
+      workflow: { research: true },
+    }, null, 2));
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as Array<Record<string, unknown>>;
+    expect(warnings.some(w => w.code === 'W008')).toBe(true);
+  });
+
+  it('derives status from errors (broken), warnings (degraded), none (healthy)', async () => {
+    // broken: no .planning/
+    const r1 = await validateHealth([], tmpDir);
+    expect((r1.data as Record<string, unknown>).status).toBe('broken');
+
+    // degraded: missing config.json (warning only, not error)
+    await createHealthyPlanning();
+    const { unlink } = await import('node:fs/promises');
+    await unlink(join(tmpDir, '.planning', 'config.json'));
+    const r2 = await validateHealth([], tmpDir);
+    expect((r2.data as Record<string, unknown>).status).toBe('degraded');
+
+    // healthy: all present
+    await writeFile(join(tmpDir, '.planning', 'config.json'), JSON.stringify({
+      model_profile: 'balanced',
+      workflow: { nyquist_validation: true },
+    }, null, 2));
+    const r3 = await validateHealth([], tmpDir);
+    expect((r3.data as Record<string, unknown>).status).toBe('healthy');
+  });
+
+  // ─── Repair tests ───────────────────────────────────────────────────────
+
+  it('--repair with missing config.json creates config.json with defaults', async () => {
+    await createHealthyPlanning();
+    const { unlink } = await import('node:fs/promises');
+    await unlink(join(tmpDir, '.planning', 'config.json'));
+
+    const result = await validateHealth(['--repair'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    expect(data.repairs_performed).toBeDefined();
+    const repairs = data.repairs_performed as Array<Record<string, unknown>>;
+    expect(repairs.some(r => r.action === 'createConfig' && r.success === true)).toBe(true);
+
+    // Verify file was created
+    const config = JSON.parse(await readFile(join(tmpDir, '.planning', 'config.json'), 'utf-8'));
+    expect(config.model_profile).toBe('balanced');
+    expect(config.workflow.nyquist_validation).toBe(true);
+  });
+
+  it('--repair with missing STATE.md generates minimal STATE.md', async () => {
+    await createHealthyPlanning();
+    const { unlink } = await import('node:fs/promises');
+    await unlink(join(tmpDir, '.planning', 'STATE.md'));
+
+    const result = await validateHealth(['--repair'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const repairs = data.repairs_performed as Array<Record<string, unknown>>;
+    expect(repairs.some(r => r.action === 'regenerateState' && r.success === true)).toBe(true);
+
+    // Verify file was created
+    const stateContent = await readFile(join(tmpDir, '.planning', 'STATE.md'), 'utf-8');
+    expect(stateContent).toContain('# Session State');
+    expect(stateContent).toContain('regenerated by');
+  });
+
+  it('--repair with missing nyquist key adds workflow.nyquist_validation', async () => {
+    await createHealthyPlanning();
+    await writeFile(join(tmpDir, '.planning', 'config.json'), JSON.stringify({
+      model_profile: 'balanced',
+      workflow: { research: true },
+    }, null, 2));
+
+    const result = await validateHealth(['--repair'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const repairs = data.repairs_performed as Array<Record<string, unknown>>;
+    expect(repairs.some(r => r.action === 'addNyquistKey' && r.success === true)).toBe(true);
+
+    // Verify key was added
+    const config = JSON.parse(await readFile(join(tmpDir, '.planning', 'config.json'), 'utf-8'));
+    expect(config.workflow.nyquist_validation).toBe(true);
+  });
+});