test: fix CI-only failures from mock.module leakage and sqlite3 .recover

These surfaced once the lockfile fix let CI actually run the suite (it had
been dying at setup-node before install). All are test-environment issues;
no production code changed.

- logger.dataIn leak (9 summarize-tag-stripping fails): timeline-formatting,
  claude-md-utils, and runtime-selector mocked logger via the process-global
  mock.module but never restored it (mock.restore() does NOT undo mock.module).
  A partial logger mock without dataIn leaked into later files under CI's file
  order. Snapshot the real module and re-register it in afterAll, matching the
  pattern already used by the chroma-mcp-manager tests.

- summarize-subagent-skip (4 fails, exposed by the runtime-selector restore):
  it mocked SettingsDefaultsManager but not hook-settings, and loadFromFileOnce()
  module-caches — so it depended on a leaked hook-settings mock. Mock
  hook-settings directly and restore in afterAll so it is self-contained.

- schema-repair (3 fails): repairMalformedDatabase shells out to
  `sqlite3 .recover`, which needs the dbpage vtab. The ubuntu CI runner's
  sqlite3 lacks it ("no such table: sqlite_dbpage"). Probe the capability and
  skip the repair tests when absent, mirroring the existing hasPython() guard.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

tests/cli/handlers/summarize-subagent-skip.test.ts

@@ -6,8 +6,10 @@ import { join } from 'path';
 // re-register the snapshots in afterAll so these mocks do not leak into later
 // test files (bun's mock.module is process-global; mock.restore() does NOT undo it).
 import * as realSettingsDefaultsManager from '../../../src/shared/SettingsDefaultsManager.js';
+import * as realHookSettings from '../../../src/shared/hook-settings.js';
 import * as realWorkerUtils from '../../../src/shared/worker-utils.js';
 const realSettingsSnapshot = { ...realSettingsDefaultsManager };
+const realHookSettingsSnapshot = { ...realHookSettings };
 const realWorkerUtilsSnapshot = { ...realWorkerUtils };
 
 mock.module('../../../src/shared/SettingsDefaultsManager.js', () => ({
@@ -21,6 +23,14 @@ mock.module('../../../src/shared/SettingsDefaultsManager.js', () => ({
   },
 }));
 
+// loadFromFileOnce() module-caches its result, so mocking SettingsDefaultsManager
+// alone is not enough — an earlier test may have already cached real settings.
+// Mock hook-settings directly so shouldTrackProject() always sees a string
+// CLAUDE_MEM_EXCLUDED_PROJECTS regardless of global mock/cache state.
+mock.module('../../../src/shared/hook-settings.js', () => ({
+  loadFromFileOnce: () => ({ CLAUDE_MEM_EXCLUDED_PROJECTS: '' }),
+}));
+
 const workerCallLog: Array<{ path: string; options: any }> = [];
 mock.module('../../../src/shared/worker-utils.js', () => ({
   ensureWorkerRunning: () => Promise.resolve(true),
@@ -55,6 +65,7 @@ afterEach(() => {
 
 afterAll(() => {
   mock.module('../../../src/shared/SettingsDefaultsManager.js', () => realSettingsSnapshot);
+  mock.module('../../../src/shared/hook-settings.js', () => realHookSettingsSnapshot);
   mock.module('../../../src/shared/worker-utils.js', () => realWorkerUtilsSnapshot);
 });
 

tests/hooks/runtime-selector.test.ts

@@ -1,6 +1,14 @@
 // SPDX-License-Identifier: Apache-2.0
 
-import { describe, it, expect, mock, beforeEach } from 'bun:test';
+import { describe, it, expect, mock, beforeEach, afterAll } from 'bun:test';
+
+// Snapshot real modules BEFORE mock.module mutates the live namespace, then
+// re-register in afterAll. bun's mock.module is process-global and survives
+// mock.restore(), so these would otherwise leak into later test files.
+import * as realHookSettings from '../../src/shared/hook-settings.js';
+import * as realLogger from '../../src/utils/logger.js';
+const realHookSettingsSnapshot = { ...realHookSettings };
+const realLoggerSnapshot = { ...realLogger };
 
 let mockSettings: Record<string, string> = {};
 
@@ -23,6 +31,11 @@ mock.module('../../src/utils/logger.js', () => ({
   },
 }));
 
+afterAll(() => {
+  mock.module('../../src/shared/hook-settings.js', () => realHookSettingsSnapshot);
+  mock.module('../../src/utils/logger.js', () => realLoggerSnapshot);
+});
+
 import {
   resolveRuntimeContext,
   selectRuntime,

tests/services/sqlite/schema-repair.test.ts

@@ -27,6 +27,42 @@ function hasPython(): boolean {
   }
 }
 
+// repairMalformedDatabase() shells out to `sqlite3 <db> .recover`, which depends
+// on the dbpage virtual table. Some sqlite3 CLI builds (e.g. on the ubuntu CI
+// runner) are compiled without it and fail with "no such table: sqlite_dbpage".
+// The repair feature legitimately requires that capability, so — like the
+// hasPython() guard above — we skip the repair tests when the host sqlite3
+// cannot perform .recover rather than reporting a false failure.
+function canRecoverViaSqlite3(): boolean {
+  const probe = tempDbPath();
+  try {
+    const db = new Database(probe, { create: true, readwrite: true });
+    db.run('CREATE TABLE probe(x)');
+    db.run('INSERT INTO probe(x) VALUES (1)');
+    db.close();
+    execFileSync('sqlite3', [probe, '.recover'], { stdio: 'pipe', encoding: 'utf-8' });
+    return true;
+  } catch {
+    return false;
+  } finally {
+    cleanup(probe);
+  }
+}
+
+const REPAIR_SUPPORTED = canRecoverViaSqlite3();
+
+function skipUnlessRepairable(): boolean {
+  if (!hasPython()) {
+    console.log('Python3 not available, skipping repair test');
+    return true;
+  }
+  if (!REPAIR_SUPPORTED) {
+    console.log("sqlite3 CLI lacks .recover (no sqlite_dbpage), skipping repair test");
+    return true;
+  }
+  return false;
+}
+
 function corruptDbViaPython(dbPath: string): void {
   const script = join(tmpdir(), `corrupt-${Date.now()}.py`);
   writeFileSync(script, `
@@ -50,8 +86,7 @@ c.close()
 
 describe('Schema repair on malformed database', () => {
   it('should repair a database with an orphaned index referencing a non-existent column', () => {
-    if (!hasPython()) {
-      console.log('Python3 not available, skipping test');
+    if (skipUnlessRepairable()) {
       return;
     }
 
@@ -120,8 +155,7 @@ describe('Schema repair on malformed database', () => {
   });
 
   it('should repair a corrupted DB that has no schema_versions table', () => {
-    if (!hasPython()) {
-      console.log('Python3 not available, skipping test');
+    if (skipUnlessRepairable()) {
       return;
     }
 
@@ -172,8 +206,7 @@ c.close()
   });
 
   it('should preserve existing data through repair and re-migration', () => {
-    if (!hasPython()) {
-      console.log('Python3 not available, skipping test');
+    if (skipUnlessRepairable()) {
       return;
     }
 

tests/shared/timeline-formatting.test.ts

@@ -1,4 +1,12 @@
-import { describe, it, expect, mock, afterEach } from 'bun:test';
+import { describe, it, expect, mock, afterEach, afterAll } from 'bun:test';
+
+// Snapshot the real logger BEFORE mock.module mutates the live namespace, then
+// re-register it in afterAll. bun's mock.module is process-global and
+// mock.restore() does NOT undo it, so a partial logger mock here would
+// otherwise leak into later test files (e.g. summarize-tag-stripping, which
+// needs logger.dataIn).
+import * as realLogger from '../../src/utils/logger.js';
+const realLoggerSnapshot = { ...realLogger };
 
 mock.module('../../src/utils/logger.js', () => ({
   logger: {
@@ -16,6 +24,10 @@ afterEach(() => {
   mock.restore();
 });
 
+afterAll(() => {
+  mock.module('../../src/utils/logger.js', () => realLoggerSnapshot);
+});
+
 describe('extractFirstFile', () => {
   const cwd = '/Users/test/project';
 

tests/utils/claude-md-utils.test.ts

@@ -1,8 +1,18 @@
-import { describe, it, expect, mock, afterEach, beforeEach } from 'bun:test';
+import { describe, it, expect, mock, afterEach, afterAll, beforeEach } from 'bun:test';
 import { mkdirSync, writeFileSync, readFileSync, existsSync, rmSync } from 'fs';
 import path, { join } from 'path';
 import { tmpdir } from 'os';
 
+// Snapshot the real modules BEFORE mock.module mutates the live namespace, then
+// re-register them in afterAll. bun's mock.module is process-global and
+// mock.restore() does NOT undo it, so a partial logger mock here would
+// otherwise leak into later test files (e.g. summarize-tag-stripping, which
+// needs logger.dataIn).
+import * as realLogger from '../../src/utils/logger.js';
+import * as realWorkerUtils from '../../src/shared/worker-utils.js';
+const realLoggerSnapshot = { ...realLogger };
+const realWorkerUtilsSnapshot = { ...realWorkerUtils };
+
 mock.module('../../src/utils/logger.js', () => ({
   logger: {
     info: () => {},
@@ -30,6 +40,11 @@ mock.module('../../src/shared/worker-utils.js', () => ({
   buildWorkerUrl: (apiPath: string) => `http://127.0.0.1:37777${apiPath}`,
 }));
 
+afterAll(() => {
+  mock.module('../../src/utils/logger.js', () => realLoggerSnapshot);
+  mock.module('../../src/shared/worker-utils.js', () => realWorkerUtilsSnapshot);
+});
+
 import {
   replaceTaggedContent,
   formatTimelineForClaudeMd,