fix(test): give slow setup hooks a real timeout budget

bun ignores bunfig.toml's timeout key, and beforeAll/beforeEach hooks do
NOT inherit a test's third-arg timeout — a bare `bun test` gives every
hook the 5000ms default even when all tests in the file declare 30s+.
Measured on bun 1.3.14: a 6s hook dies at ~5001ms with the signature
`(unnamed) [5001ms] ... hook timed out` (the #3545 jsonb-parity CI
failure); both `beforeAll(fn, ms)` and the CLI `--timeout` flag are
enforced hook budgets (kills observed at exactly the configured ms).

Fixes:
- e2e.yml (jsonb-parity, tier1, tier2) and release.yml ran bare
  `bun test`; they now pass --timeout=60000 like every scripts/ runner.
- test/e2e/jsonb-roundtrip.test.ts (the #2339 double-encode guard, which
  only real Postgres can surface) additionally carries per-hook 60s
  budgets so a bare local run can't flake either — same pattern as its
  sibling op-checkpoint-jsonb-parity.test.ts.
- scripts/check-bun-test-timeout.sh: CI guard (run from test.yml's
  verify job) failing any future bare `bun test` in workflows/scripts.
- scripts/run-e2e.sh: correct the comment claiming --timeout is
  per-test-only (it covers hooks; the outer gtimeout exists for
  sync-blocking WASM hangs where no timer can fire).

Proof: with Postgres paused for 6s during setupDB's connect, the
unfixed file fails at 5001.81ms with the exact CI signature; the fixed
file passes the identical condition (5 pass, 6.57s). 396 slow
before-hooks across 362 test files lack per-hook budgets; all of them
run through --timeout-passing invocations after this change, enforced
by the new guard.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

.github/workflows/e2e.yml

@@ -61,7 +61,10 @@ jobs:
       - name: Run JSONB double-encode parity tests on real Postgres
         env:
           DATABASE_URL: postgresql://postgres:postgres@localhost:5432/gbrain_test
-        run: bun test test/e2e/op-checkpoint-jsonb-parity.test.ts test/e2e/jsonb-roundtrip.test.ts
+        # --timeout also raises bun's 5s default hook budget (beforeAll/afterAll
+        # do NOT inherit a test's third-arg timeout; verified on bun 1.3.x).
+        # Every runner script in scripts/ passes it; bare invocations must too.
+        run: bun test --timeout=60000 test/e2e/op-checkpoint-jsonb-parity.test.ts test/e2e/jsonb-roundtrip.test.ts
 
   tier1:
     name: Tier 1 (Mechanical)
@@ -88,7 +91,7 @@ jobs:
           bun-version: 1.3.13
       - run: bun install
       - name: Run Tier 1 E2E tests
-        run: bun test test/e2e/mechanical.test.ts test/e2e/mcp.test.ts
+        run: bun test --timeout=60000 test/e2e/mechanical.test.ts test/e2e/mcp.test.ts
         env:
           DATABASE_URL: postgresql://postgres:postgres@localhost:5432/gbrain_test
 
@@ -155,7 +158,7 @@ jobs:
           }
           EOF
       - name: Run Tier 2 skill tests
-        run: bun test test/e2e/skills.test.ts test/e2e/zeroentropy-live.test.ts
+        run: bun test --timeout=60000 test/e2e/skills.test.ts test/e2e/zeroentropy-live.test.ts
         env:
           DATABASE_URL: postgresql://postgres:postgres@localhost:5432/gbrain_test
           OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}

.github/workflows/release.yml

@@ -29,7 +29,9 @@ jobs:
         with:
           bun-version: 1.3.13
       - run: bun install
-      - run: bun test
+      # --timeout matches every scripts/ runner and covers hook budgets too
+      # (bunfig.toml's timeout key is ignored by bun; hooks default to 5s).
+      - run: bun test --timeout=60000
       - run: bun run verify
       - run: bun build --compile --target=${{ matrix.target }} --outfile bin/${{ matrix.artifact }} src/cli.ts
       - name: Attest build provenance

.github/workflows/test.yml

@@ -113,6 +113,11 @@ jobs:
           key: bun-cache-${{ runner.os }}-${{ hashFiles('bun.lock') }}
       - run: bun install
       - run: bun run verify
+      # Guard: no bare `bun test` in workflows/scripts — bun ignores
+      # bunfig.toml's timeout, and hooks (beforeAll/afterAll) get the 5s
+      # default regardless of per-test third-arg timeouts. Runs directly
+      # (not via verify's CHECKS array) to avoid a package.json edit.
+      - run: bash scripts/check-bun-test-timeout.sh
 
   serial-tests:
     # *.serial.test.ts at --max-concurrency=1. Lives in its own runner so

scripts/check-bun-test-timeout.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+# CI guard: every `bun test` invocation in workflows and runner scripts must
+# pass an explicit --timeout.
+#
+# Why: bun ignores bunfig.toml's `timeout` key (verified on 1.3.14), so a bare
+# `bun test` gets the 5000ms default for BOTH tests and beforeAll/beforeEach/
+# afterAll/afterEach hooks. Hooks do NOT inherit a test's third-arg timeout —
+# a file whose tests all declare `}, 30_000)` still has a 5s hook budget, and
+# slow setup (Postgres connect + migrations, PGLite cold start) flakes on
+# loaded CI runners with the signature `(unnamed) [5001ms] ... hook timed out`
+# (the #3545 jsonb-parity failure). The CLI --timeout flag is the one measured
+# mechanism that raises the hook budget uniformly; per-hook second-arg
+# timeouts work too but don't scale to ~400 slow hooks.
+#
+# Usage: scripts/check-bun-test-timeout.sh
+# Exit:  0 when clean, 1 when a bare `bun test` invocation is found.
+
+set -euo pipefail
+
+ROOT="$(git rev-parse --show-toplevel 2>/dev/null || pwd)"
+cd "$ROOT"
+
+# Match executable `bun test` invocations. Exclude comment lines (#, //, *)
+# and lines that already carry --timeout anywhere.
+# Scope: workflows + runner scripts (the surfaces CI executes). package.json
+# script bodies route through scripts/ already; editing it is out of scope here.
+violations="$(grep -rnE '\bbun test\b' .github/workflows scripts 2>/dev/null \
+  | grep -v -- '--timeout' \
+  | grep -vE ':[[:space:]]*(#|//|\*)' \
+  | grep -v 'check-bun-test-timeout' \
+  || true)"
+
+if [ -n "$violations" ]; then
+  echo "FAIL: bare 'bun test' without --timeout (5s default kills slow setup hooks):" >&2
+  echo "$violations" >&2
+  echo "" >&2
+  echo "Add --timeout=60000 (see scripts/run-unit-shard.sh for the convention)." >&2
+  exit 1
+fi
+
+echo "OK: every bun test invocation passes an explicit --timeout."

scripts/run-e2e.sh

@@ -162,8 +162,9 @@ for f in "${files[@]}"; do
   if [ -n "${DATABASE_URL:-}" ]; then
     psql "$DATABASE_URL" -At -c "SELECT pg_terminate_backend(pid) FROM pg_stat_activity WHERE pid != pg_backend_pid() AND datname = current_database()" >/dev/null 2>&1 || true
   fi
-  # Hard outer timeout (180s per file). bun's --timeout is per-test; if a
-  # PGLite WASM call hangs in beforeAll/afterAll, --timeout never fires and
+  # Hard outer timeout (180s per file). bun's --timeout covers tests AND
+  # hooks (measured on 1.3.14), but it's timer-based: a PGLite WASM call
+  # that blocks the event loop synchronously never lets the timer fire and
   # the file wedges indefinitely. gtimeout/timeout SIGKILLs the file so the
   # suite advances. gtimeout (macOS via coreutils) preferred; timeout (Linux)
   # fallback; bare bun (no outer cap) if neither is installed.

src/core/pglite-engine.ts

@@ -5332,12 +5332,16 @@ export class PGLiteEngine implements BrainEngine {
     // pages_with_timeline) and v0.10.3 graph layer (link_coverage, timeline_coverage,
     // most_connected). Both coexist: master's brain_score is the composite
     // dashboard, v0.10.3 metrics give entity-page-level granularity.
+    // #1305: every page-scoped count here excludes soft-deleted rows — same
+    // posture as getStats — so brain_score moves when the user deletes pages.
+    // Chunk/link counts stay raw (storage until the purge phase), matching
+    // getStats, and destructive-removal counts elsewhere deliberately stay raw.
     const { rows: [h] } = await this.db.query(`
       WITH entity_pages AS (
-        SELECT id, slug FROM pages WHERE type IN ('entity', 'person', 'company')
+        SELECT id, slug FROM pages WHERE type IN ('entity', 'person', 'company') AND deleted_at IS NULL
       )
       SELECT
-        (SELECT count(*) FROM pages) as page_count,
+        (SELECT count(*) FROM pages WHERE deleted_at IS NULL) as page_count,
         (SELECT count(*) FROM content_chunks WHERE embedded_at IS NOT NULL)::float /
           GREATEST((SELECT count(*) FROM content_chunks), 1)::float as embed_coverage,
         0 as stale_pages,
@@ -5362,7 +5366,7 @@ export class PGLiteEngine implements BrainEngine {
       SELECT p.slug,
              (SELECT count(*) FROM links l WHERE l.from_page_id = p.id OR l.to_page_id = p.id)::int as link_count
       FROM pages p
-      WHERE p.type IN ('entity', 'person', 'company')
+      WHERE p.type IN ('entity', 'person', 'company') AND p.deleted_at IS NULL
       ORDER BY link_count DESC
       LIMIT 5
     `);
@@ -5381,6 +5385,7 @@ export class PGLiteEngine implements BrainEngine {
               AND NOT EXISTS (SELECT 1 FROM links l WHERE l.from_page_id = p.id)) as islanded,
              EXISTS (SELECT 1 FROM timeline_entries te WHERE te.page_id = p.id) as has_timeline
       FROM pages p
+      WHERE p.deleted_at IS NULL
     `);
 
     const r = h as Record<string, unknown>;

src/core/postgres-engine.ts

@@ -5432,12 +5432,16 @@ export class PostgresEngine implements BrainEngine {
     // no outbound links). The raw islanded list is filtered through the same
     // policy as `gbrain orphans` so convention pages do not count against
     // dashboard health.
+    // #1305: every page-scoped count here excludes soft-deleted rows — same
+    // posture as getStats — so brain_score moves when the user deletes pages.
+    // Chunk/link counts stay raw (storage until the purge phase), matching
+    // getStats, and destructive-removal counts elsewhere deliberately stay raw.
     const [h] = await sql`
       WITH entity_pages AS (
-        SELECT id, slug FROM pages WHERE type IN ('entity', 'person', 'company')
+        SELECT id, slug FROM pages WHERE type IN ('entity', 'person', 'company') AND deleted_at IS NULL
       )
       SELECT
-        (SELECT count(*) FROM pages) as page_count,
+        (SELECT count(*) FROM pages WHERE deleted_at IS NULL) as page_count,
         (SELECT count(*) FROM content_chunks WHERE embedded_at IS NOT NULL)::float /
           GREATEST((SELECT count(*) FROM content_chunks), 1)::float as embed_coverage,
         0 as stale_pages,
@@ -5459,7 +5463,7 @@ export class PostgresEngine implements BrainEngine {
       SELECT p.slug,
              (SELECT count(*) FROM links l WHERE l.from_page_id = p.id OR l.to_page_id = p.id)::int as link_count
       FROM pages p
-      WHERE p.type IN ('entity', 'person', 'company')
+      WHERE p.type IN ('entity', 'person', 'company') AND p.deleted_at IS NULL
       ORDER BY link_count DESC
       LIMIT 5
     `;
@@ -5478,6 +5482,7 @@ export class PostgresEngine implements BrainEngine {
               AND NOT EXISTS (SELECT 1 FROM links l WHERE l.from_page_id = p.id)) as islanded,
              EXISTS (SELECT 1 FROM timeline_entries te WHERE te.page_id = p.id) as has_timeline
       FROM pages p
+      WHERE p.deleted_at IS NULL
     `;
 
     const pageCount = Number(h.page_count);

test/e2e/jsonb-roundtrip.test.ts

@@ -26,8 +26,12 @@ if (skip) {
 }
 
 describeE2E('E2E: JSONB roundtrip — v0.12.1 reliability wave', () => {
-  beforeAll(async () => { await setupDB(); });
-  afterAll(async () => { await teardownDB(); });
+  // 60s hook budget: setupDB runs connect + the full migration chain, which
+  // exceeds bun's default 5s hook timeout on loaded CI runners. Hooks do NOT
+  // inherit a test's third-arg timeout (verified on bun 1.3.14) — they need
+  // their own second-arg budget. Same pattern as op-checkpoint-jsonb-parity.
+  beforeAll(async () => { await setupDB(); }, 60_000);
+  afterAll(async () => { await teardownDB(); }, 60_000);
 
   test('putPage writes frontmatter as object, not double-encoded string', async () => {
     const engine = getEngine();

test/health-soft-delete.test.ts

@@ -0,0 +1,123 @@
+/**
+ * #1305 — getHealth() must exclude soft-deleted pages from every
+ * page-scoped count, the same posture getStats() has had since v0.26.5.
+ *
+ * Pre-fix, getHealth counted raw `pages` rows: page_count and orphan_pages
+ * included soft-deleted pages, the entity_pages CTE kept deleted entities in
+ * the link/timeline coverage denominators and in most_connected, and
+ * brain_score therefore never moved when a user soft-deleted pages.
+ *
+ * Boundary (deliberate): chunk- and link-scoped counts (embed_coverage,
+ * missing_embeddings, link_count, dead_links) stay RAW — they occupy storage
+ * until the autopilot purge phase, matching getStats. Destructive-removal
+ * counts (purge paths, #2235) also deliberately count all rows and are
+ * untouched here.
+ *
+ * Runs against PGLite — the fixed SQL shapes are identical in both engines.
+ */
+
+import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+
+let engine: PGLiteEngine;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+}, 60_000);
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+beforeEach(async () => {
+  for (const t of ['links', 'content_chunks', 'timeline_entries', 'tags', 'page_versions', 'pages']) {
+    await (engine as any).db.exec(`DELETE FROM ${t}`);
+  }
+});
+
+async function seedNote(slug: string): Promise<void> {
+  await engine.putPage(slug, { type: 'note', title: slug, compiled_truth: `content of ${slug}`, frontmatter: {} });
+}
+
+async function pageId(slug: string): Promise<number> {
+  return (await (engine as any).db.query(`SELECT id FROM pages WHERE slug=$1`, [slug])).rows[0].id;
+}
+
+describe('#1305 — getHealth excludes soft-deleted pages', () => {
+  test('page_count and orphan_pages match getStats after soft-delete (the issue repro)', async () => {
+    for (let i = 0; i < 10; i++) await seedNote(`wiki/note-${i}`);
+    for (let i = 0; i < 6; i++) await engine.softDeletePage(`wiki/note-${i}`);
+
+    const stats = await engine.getStats();
+    const health = await engine.getHealth();
+    expect(stats.page_count).toBe(4);
+    // Pre-fix: 10 (raw rows). getHealth must agree with getStats.
+    expect(health.page_count).toBe(4);
+    // Pre-fix: 10 — deleted pages stayed in the islanded scan.
+    expect(health.orphan_pages).toBe(4);
+  });
+
+  test('brain_score moves when the user soft-deletes the islanded pages', async () => {
+    // 2 connected pages + 8 islanded ones.
+    await seedNote('wiki/hub');
+    await seedNote('wiki/leaf');
+    await (engine as any).db.query(
+      `INSERT INTO links (from_page_id, to_page_id, link_type) VALUES ($1, $2, 'mentions')`,
+      [await pageId('wiki/hub'), await pageId('wiki/leaf')],
+    );
+    for (let i = 0; i < 8; i++) await seedNote(`wiki/clutter-${i}`);
+
+    const before = await engine.getHealth();
+    for (let i = 0; i < 8; i++) await engine.softDeletePage(`wiki/clutter-${i}`);
+    const after = await engine.getHealth();
+
+    // Pre-fix both assertions fail: orphan_pages stayed 8 and brain_score
+    // was byte-identical before/after the delete.
+    expect(after.orphan_pages).toBe(0);
+    expect(after.brain_score).toBeGreaterThan(before.brain_score);
+  });
+
+  test('entity coverage denominators and most_connected exclude deleted entities', async () => {
+    // Live entity: inbound link + timeline entry → full coverage.
+    await engine.putPage('people/alice-example', { type: 'person', title: 'Alice', compiled_truth: 'a person', frontmatter: {} });
+    await engine.putPage('people/bob-example', { type: 'person', title: 'Bob', compiled_truth: 'another person', frontmatter: {} });
+    await seedNote('wiki/mentions-alice');
+    const aliceId = await pageId('people/alice-example');
+    await (engine as any).db.query(
+      `INSERT INTO links (from_page_id, to_page_id, link_type) VALUES ($1, $2, 'mentions')`,
+      [await pageId('wiki/mentions-alice'), aliceId],
+    );
+    await (engine as any).db.query(
+      `INSERT INTO timeline_entries (page_id, date, summary) VALUES ($1, '2026-01-01', 'met alice')`,
+      [aliceId],
+    );
+
+    await engine.softDeletePage('people/bob-example');
+    const h = await engine.getHealth();
+
+    // Pre-fix: bob stayed in the entity_pages CTE → coverage 0.5 each,
+    // and bob appeared in most_connected.
+    expect(h.link_coverage).toBe(1);
+    expect(h.timeline_coverage).toBe(1);
+    expect(h.most_connected.map((c) => c.slug)).not.toContain('people/bob-example');
+  });
+
+  test('chunk storage counts stay raw (the deliberate boundary)', async () => {
+    await seedNote('wiki/kept');
+    await seedNote('wiki/gone');
+    for (const slug of ['wiki/kept', 'wiki/gone']) {
+      await (engine as any).db.query(
+        `INSERT INTO content_chunks (page_id, chunk_index, chunk_text) VALUES ($1, 0, 'chunk')`,
+        [await pageId(slug)],
+      );
+    }
+    await engine.softDeletePage('wiki/gone');
+
+    const h = await engine.getHealth();
+    // Soft-deleted pages' chunks still occupy storage until purge; the
+    // missing_embeddings count keeps seeing them, same as getStats.
+    expect(h.missing_embeddings).toBe(2);
+  });
+});