Refactor SDK-first architecture seams (#3316)

* refactor: tighten sdk-first architecture seams

Refs #3312

* refactor: finish state document seam cleanup

Refs #3312

* test: harden minimal install cleanup assertion

* ci: support sdk-scoped package lock

* fix(3316): restore root package-lock.json and align changeset pr ref

Reverts dec57a83 ("ci: support sdk-scoped package lock") and restores
the root package-lock.json that c249d34d deleted. The deletion was the
wrong direction:

- The root package.json declares its own runtime and dev deps
  (@anthropic-ai/claude-agent-sdk, ws, c8). Without a root lockfile,
  `npm install --no-package-lock` resolves whatever satisfies semver at
  install time — CI today and CI in six months can install different
  transitive trees, defeating reproducibility.
- The lockfile has been part of every release on this repo (long
  history on main); removing it loses the npm audit / Dependabot
  target without compensating benefit.
- The CI workaround pattern (cache-dependency-path: sdk/package-lock.json
  + `npm install --no-package-lock`) papered over the symptom rather
  than fix the cause.

Also fix the changeset pr: from 3312 (issue) to 3316 (PR). CONTEXT.md
flags this exact failure mode as a recurring CodeRabbit finding.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix: address coderabbit review findings

* fix: close remaining coderabbit threads

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

sdk/src/query/state.test.ts

@@ -155,8 +155,36 @@ describe('stateJson', () => {
     expect(progress.completed_plans).toBe(4);
     // Phase 09 complete (3/3), phase 10 incomplete (1/3), phase 11 incomplete (0/1)
     expect(progress.completed_phases).toBe(1);
-    // 4/7 = 57%
-    expect(progress.percent).toBe(57);
+    // min(plan fraction 4/7, phase fraction 1/3) = 33%
+    expect(progress.percent).toBe(33);
+  });
+
+  it('preserves wider curated progress when disk scan only sees a realized subset', async () => {
+    const stateContent = `---
+gsd_state_version: 1.0
+milestone: v3.0
+milestone_name: SDK-First Migration
+status: executing
+progress:
+  total_phases: 12
+  completed_phases: 6
+  total_plans: 22
+  completed_plans: 22
+  percent: 50
+---
+
+${STATE_BODY}`;
+    await writeFile(join(tmpDir, '.planning', 'STATE.md'), stateContent);
+
+    const result = await stateJson([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const progress = data.progress as Record<string, unknown>;
+
+    expect(progress.total_phases).toBe(12);
+    expect(progress.completed_phases).toBe(6);
+    expect(progress.total_plans).toBe(22);
+    expect(progress.completed_plans).toBe(22);
+    expect(progress.percent).toBe(50);
   });
 
   it('preserves stopped_at from existing frontmatter', async () => {
@@ -232,8 +260,8 @@ Progress: [░░░░░░░░░░] 0%
     const data = result.data as Record<string, unknown>;
     const progress = data.progress as Record<string, unknown>;
 
-    // Disk should override the body's 0%
-    expect(progress.percent).toBe(57);
+    // Disk should override the body's 0%; phase fraction caps plan-only progress.
+    expect(progress.percent).toBe(33);
   });
 });