fix(tests): bump phase-count assertions from 17→19 (v0.41 follow-on)

v0.41 added extract_atoms + synthesize_concepts to ALL_PHASES.
Three existing tests pinned the count at 17 via load-bearing
regression assertions:

  test/phase-scope-coverage.test.ts:48-49
    expect(ALL_PHASES.length).toBe(17)
    expect(Object.keys(PHASE_SCOPE).length).toBe(17)

  test/core/cycle.serial.test.ts:393
    expect(hookCalls).toBe(17)  // yieldBetweenPhases hook fires per phase

  test/core/cycle.serial.test.ts:406
    expect(report.phases.length).toBe(17)

  test/e2e/cycle.test.ts:110
    expect(report.phases.length).toBe(17)

These are the correct fix: the assertions exist precisely to catch
this case (a PR that adds a phase without updating downstream
consumers). The wave's v0.41 commit (T9) updated ALL_PHASES but
missed these three sites. Updating them to 19 with comment
breadcrumbs preserving the version history (v0.26.5 → 9,
v0.29 → 10, v0.31 → 11, v0.32.2 → 12, v0.33.3 → 13,
v0.36.1.0 → 16, v0.39.0.0 → 17, v0.41.0.0 → 19).

Without this fix: full unit test suite (`bun run test`) shows 3
failures from these assertions. Underlying v0.41 logic was already
green; this is pure pin-bumping.

After fix: 9059 unit tests pass. 0 actual test failures. (3 shard
wedges remain from unrelated long-running parallel-runner tests
that exceed the 600s per-shard cap — infra concern, not test
logic, pre-dates this wave.)

Plan: ~/.claude/plans/system-instruction-you-are-working-toasty-milner.md
Wave gate: all 13 plan tasks done; all v0.41 tests pass.

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

test/core/cycle.serial.test.ts

@@ -390,7 +390,8 @@ describe('runCycle — yieldBetweenPhases hook', () => {
     // v0.33.3: 13 phases (added `resolve_symbol_edges` between extract_facts and patterns) → 13 yield calls.
     // v0.36.1.0: 16 phases (added `propose_takes`, `grade_takes`, `calibration_profile` between consolidate and embed).
     // v0.39.0.0: 17 phases (added `schema-suggest` between orphans and purge — T12 schema cathedral).
-    expect(hookCalls).toBe(17);
+    // v0.41.0.0: 19 phases (added `extract_atoms` after extract_facts + `synthesize_concepts` after patterns).
+    expect(hookCalls).toBe(19);
   });
 
   test('hook exceptions do not abort the cycle', async () => {
@@ -403,7 +404,7 @@ describe('runCycle — yieldBetweenPhases hook', () => {
     // v0.33.3: 13 phases (v0.32.2's 12 + resolve_symbol_edges).
     // v0.36.1.0: 16 phases (Hindsight calibration wave adds propose_takes, grade_takes, calibration_profile).
     // v0.39.0.0: 17 phases (T12 schema-suggest phase between orphans and purge).
-    expect(report.phases.length).toBe(17);
+    expect(report.phases.length).toBe(19); // v0.41: +extract_atoms, +synthesize_concepts
   });
 });
 

test/e2e/cycle.test.ts

@@ -107,7 +107,7 @@ describeE2E('E2E: runCycle against real Postgres', () => {
     //   v0.33.3   = 13 (added `resolve_symbol_edges` between extract_facts and patterns)
     //   v0.36.1.0 = 16 (added propose_takes + grade_takes + calibration_profile — hindsight calibration wave)
     //   v0.39.0.0 = 17 (added `schema-suggest` between orphans and purge — T12 schema cathedral)
-    expect(report.phases.length).toBe(17);
+    expect(report.phases.length).toBe(19); // v0.41: +extract_atoms, +synthesize_concepts
 
     // Nothing got written.
     const afterPages = await conn.unsafe(`SELECT count(*)::int AS n FROM pages`);

test/phase-scope-coverage.test.ts

@@ -41,12 +41,13 @@ describe('PHASE_SCOPE coverage', () => {
     expect(invalid).toEqual([]);
   });
 
-  test('all 17 phases covered (regression on accidental omission)', () => {
+  test('all 19 phases covered (regression on accidental omission)', () => {
     // Pin the count so a future PR that adds a phase to ALL_PHASES
     // without updating PHASE_SCOPE notices here too. The v0.39.1.0
-    // master merge brought in the 17th phase (`schema-suggest`).
-    expect(ALL_PHASES.length).toBe(17);
-    expect(Object.keys(PHASE_SCOPE).length).toBe(17);
+    // master merge brought in the 17th phase (`schema-suggest`); v0.41
+    // adds 'extract_atoms' + 'synthesize_concepts' for a total of 19.
+    expect(ALL_PHASES.length).toBe(19);
+    expect(Object.keys(PHASE_SCOPE).length).toBe(19);
   });
 
   test('embed remains global (the headline brain-wide phase)', () => {