chore(release): 10.4.11

The single-flight gate queued its follow-up as
`leader.catch().then(() => this.flush())`. That waiter is settled ONLY by
resolving the very promise the leader is being awaited through, so the moment
anything inside a flush body awaits flush(), the promise graph closes on itself
and nobody resolves — an unbounded hang, not a slow flush, presenting exactly
like a bulk write timing out. No current call site awaits a flush from inside
one, so this is a latent cycle rather than an observed one; the gate should not
depend on that staying true.

The queue is now a bare deferred. The leader's finally opens the gate and
PROMOTES the waiter to a new leader, settling the deferred from that run; the
finally returns nothing, so the leader never awaits its own follower. Every
exit runs the same promotion — the leader resolving, the leader rejecting, the
promoted run rejecting — so a queued caller is settled exactly once on every
path, and a synchronous failure starting the promoted run is reported to the
waiter instead of thrown into the leader's finally. close() drains both handles.

tests/unit/brainy/flush-single-flight.test.ts pins the invariant on each path
that must settle a waiter: many callers during one flush all resolve within a
bound (one body, one follow-up, peak concurrency 1); a REJECTING leader still
runs and settles the queued waiter; a rejecting follow-up settles its waiter
and leaves the gate open; and the leader returns without waiting for a
deliberately slower follower.

.forgejo/workflows/ci.yml

@@ -5,6 +5,10 @@ name: CI
 # sequential, so tag-triggered matrix jobs (~22 min) would queue AHEAD of the
 # tag's publish-source run and starve every release (observed on 8.10.3 and
 # 9.0.0: the publish sat behind the tag's own redundant CI).
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
 on:
   push:
     branches: ['**']

.forgejo/workflows/delta-gate.yml

@@ -0,0 +1,148 @@
+name: Delta Gate
+
+# On-demand candidate-vs-control gate on the capped functional CI lane
+# (label: gate-functional). That lane is Bun-only host-mode — there is no
+# Node.js runtime available to it, so this workflow deliberately avoids every
+# JS-based action (checkout/setup-node/setup-bun/upload-artifact all require
+# one) and does everything with plain git + bun in shell steps instead.
+#
+# Verdict lines a caller should grep for in the run log:
+#   COLLECTED patch=<n> control=<n>   — collection-truncation guard inputs
+#   NEW-RED-COUNT:<n>                 — failures on candidate absent from control
+#   DELTA-GATE: CLEAN | NEW REDS | INVALID | STOPPED-BY-REGISTRY-TRIPWIRE
+#
+# The lane's own housekeeping stops the runner and drops a marker file when
+# host pressure (I/O, registry latency, disk budget) trips — never ours to
+# interpret as a red or a green. The final step checks for that marker before
+# it says anything about pass/fail.
+
+on:
+  workflow_dispatch:
+    inputs:
+      candidate:
+        description: 'Candidate ref (branch or sha) to gate'
+        required: true
+        type: string
+      control:
+        description: 'Control sha to diff against'
+        required: true
+        type: string
+  # workflow_dispatch needs Actions-unit write on the dispatching credential;
+  # push does not (it runs from the pushed ref's own tree), so a plain push
+  # to a release or CI branch is the fallback trigger while that grant is
+  # outstanding — see the ref-resolution step below for what it gates against.
+  push:
+    branches: ['rel/**', 'ci/**']
+
+concurrency:
+  group: delta-gate
+  cancel-in-progress: false
+
+jobs:
+  delta-gate:
+    name: Delta gate — candidate vs control
+    runs-on: gate-functional
+    timeout-minutes: 120
+    steps:
+      - name: Resolve candidate/control refs
+        id: refs
+        run: |
+          candidate="${{ github.event.inputs.candidate }}"
+          control="${{ github.event.inputs.control }}"
+          # workflow_dispatch supplies both explicitly; a push event carries
+          # neither — fall back to the pushed commit as candidate and the
+          # last released, known-good tip (10.4.9) as control, so a plain
+          # push still produces a meaningful gate instead of an empty ref.
+          if [ -z "$candidate" ]; then candidate="${{ github.sha }}"; fi
+          if [ -z "$control" ]; then control="eec90bdd"; fi
+          echo "candidate=$candidate" >> "$GITHUB_OUTPUT"
+          echo "control=$control" >> "$GITHUB_OUTPUT"
+          echo "Resolved (trigger=${{ github.event_name }}): candidate=$candidate control=$control"
+
+      - name: Clean any residue from a prior run
+        run: rm -rf "ob-cand-${{ github.run_id }}" "ob-ctrl-${{ github.run_id }}" "/tmp/ob-${{ github.run_id }}-"*
+
+      - name: Clone + test — candidate
+        id: patch
+        run: |
+          set -o pipefail
+          git clone --quiet "https://source.soulcraft.com/soulcraftlabs/open-brainy.git" "ob-cand-${{ github.run_id }}"
+          cd "ob-cand-${{ github.run_id }}"
+          git checkout --quiet "${{ steps.refs.outputs.candidate }}"
+          git log --oneline -1
+          bun install
+          rc=0
+          bun x vitest run > "/tmp/ob-${{ github.run_id }}-patch.log" 2>&1 || rc=$?
+          echo "PATCH-RC:$rc"
+          grep -aE "Tests .*(passed|failed)" "/tmp/ob-${{ github.run_id }}-patch.log" | tail -1
+          grep -aE "^ FAIL |^\s+×" "/tmp/ob-${{ github.run_id }}-patch.log" | sed -E "s/ [0-9]+ms$//" | sed -E "s/^\s+//" | sort -u > "/tmp/ob-${{ github.run_id }}-patch.fail"
+          echo "PATCH-FAILING:$(wc -l < "/tmp/ob-${{ github.run_id }}-patch.fail")"
+
+      - name: Clone + test — control
+        id: control
+        run: |
+          set -o pipefail
+          git clone --quiet "https://source.soulcraft.com/soulcraftlabs/open-brainy.git" "ob-ctrl-${{ github.run_id }}"
+          cd "ob-ctrl-${{ github.run_id }}"
+          git checkout --quiet "${{ steps.refs.outputs.control }}"
+          git log --oneline -1
+          bun install
+          rc=0
+          bun x vitest run > "/tmp/ob-${{ github.run_id }}-control.log" 2>&1 || rc=$?
+          echo "CONTROL-RC:$rc"
+          grep -aE "Tests .*(passed|failed)" "/tmp/ob-${{ github.run_id }}-control.log" | tail -1
+          grep -aE "^ FAIL |^\s+×" "/tmp/ob-${{ github.run_id }}-control.log" | sed -E "s/ [0-9]+ms$//" | sed -E "s/^\s+//" | sort -u > "/tmp/ob-${{ github.run_id }}-control.fail"
+          echo "CONTROL-FAILING:$(wc -l < "/tmp/ob-${{ github.run_id }}-control.fail")"
+
+      - name: Delta gate verdict
+        if: always()
+        run: |
+          set -o pipefail
+
+          # The lane's own tripwire wins over anything we would otherwise say:
+          # a bare failure/timeout above with this marker present is host
+          # pressure, never a real red and never a real green.
+          if [ -f /srv/gate-lane/TRIPWIRE-STOPPED ]; then
+            echo "DELTA-GATE: STOPPED-BY-REGISTRY-TRIPWIRE"
+            head -1 /srv/gate-lane/TRIPWIRE-STOPPED
+            exit 3
+          fi
+
+          patch_log="/tmp/ob-${{ github.run_id }}-patch.log"
+          control_log="/tmp/ob-${{ github.run_id }}-control.log"
+          patch_fail="/tmp/ob-${{ github.run_id }}-patch.fail"
+          control_fail="/tmp/ob-${{ github.run_id }}-control.fail"
+
+          if [ ! -s "$patch_log" ] || [ ! -s "$control_log" ]; then
+            echo "DELTA-GATE: INVALID — a leg produced no log (see the two steps above for the real cause)"
+            exit 2
+          fi
+
+          pt=$(grep -aoE "\(([0-9]+)\)$" "$patch_log" | tail -1 | tr -d "()")
+          ct=$(grep -aoE "\(([0-9]+)\)$" "$control_log" | tail -1 | tr -d "()")
+          echo "COLLECTED patch=${pt:-0} control=${ct:-0}"
+          if [ "${pt:-0}" -lt 3000 ] || [ "${ct:-0}" -lt 3000 ]; then
+            echo "DELTA-GATE: INVALID — truncated collection"
+            exit 2
+          fi
+
+          echo "=== NEW REDS ==="
+          comm -23 "$patch_fail" "$control_fail"
+          new=$(comm -23 "$patch_fail" "$control_fail" | wc -l)
+          echo "NEW-RED-COUNT:$new"
+
+          echo "=== full candidate fail list ==="
+          cat "$patch_fail"
+          echo "=== full control fail list ==="
+          cat "$control_fail"
+
+          if [ "$new" -eq 0 ]; then
+            echo "DELTA-GATE: CLEAN"
+          else
+            echo "DELTA-GATE: NEW REDS"
+            exit 1
+          fi
+
+      - name: Clean up (mind the lane's disk budget)
+        if: always()
+        run: rm -rf "ob-cand-${{ github.run_id }}" "ob-ctrl-${{ github.run_id }}" "/tmp/ob-${{ github.run_id }}-"*

CHANGELOG.md

@@ -2,6 +2,58 @@
 
 All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines.
 
+### [10.4.11](https://source.soulcraft.com/soulcraftlabs/open-brainy/compare/v10.4.9...v10.4.11) (2026-09-02)
+
+- ci: superseded pushes cancel their own runs (concurrency per ref) (6053f6d4)
+- test(batch): the batch-size-limit tests add unvectored items — they test batching, not embedding (a1423c6d)
+- fix(flush): the gate settles its waiter from the machine, never from a chain (dea3ec20)
+- test(batch): the batch-vs-individual timing assertion runs in the perf lane, not the correctness gate (ebb3a4bf)
+- test(gate): the coverage guard counts the perf lane's config as a gate (2c5e3474)
+- chore(contract): emit the 10.4.11 manifest (4142f368)
+- fix(close): a read-only brain writes no clean-shutdown evidence — the marker is the writer's word about itself (367ca721)
+- fix(generation-store): commitTransaction refuses while single-ops are pending — the order invariant is enforced, not assumed (a79db434)
+- test(shutdown): pin one owner per brain — real processes, real signals (da951990)
+- fix(shutdown): one owner per brain — the signal handler defers to close(), and flush is single-flight (ec644bde)
+- fix(vfs): a path-scoped search is a served range over the path, not a refused prefix match (65493ba2)
+- ci(test): perf and scale benchmarks leave the correctness gate (dee46b35)
+- test(open): pin the pending-embed checkpoint — stuck id, crash matrix, torn fallback (1fb51093)
+- perf(open): the pending-embed fold is bounded by a checkpoint of the SET, not an empty-only mark (15d4f65d)
+- perf(open): a sealed segment the manifest proves is below the bound is never read (bc70c43d)
+- fix(find): a page the metadata block already cut is not cut again (905c267c)
+- fix(find): the hybrid legs rank inside the filter, and only the page is read (b1c70544)
+- ci(delta-gate): add a push fallback trigger alongside workflow_dispatch (67ae0046)
+- ci: add the delta-gate workflow for the capped functional lane (9922631d)
+- docs(plugin): the planner door's hiddenIds contract is the answer, not the mechanism (2633e8d5)
+- feat(engine): a protected factory for the generation store — a subclass may substitute one that keeps the contract (f763317a)
+- fix(find): near() searches around the anchor's own vector, and refuses by name without one (a8c5fbf9)
+- Merge remote-tracking branches 'origin/fix/planner-provider-door' and 'origin/fix/containment-batching' into rel/10.4.10-candidate (34f1886f)
+- feat(plugin): an optional planFindPage door — an index that can plan a find answers it in one call (4d5f823f)
+- perf(vfs): repairContainment's reconcile is one paged edge walk, not one graph call per file (3e60aded)
+
+
+### [10.4.9](https://source.soulcraft.com/soulcraftlabs/open-brainy/compare/v10.4.6...v10.4.9) (2026-09-02)
+
+- Merge branch 'fix/pending-embed-low-water' into rel/10.4.9-candidate (2648f56d)
+- fix(open): pending-embed recovery keeps the crash-recovery contract — foreground, bounded by the mark (8a2ebacf)
+- Merge branches 'fix/connected-find-order', 'fix/pending-embed-low-water' and 'fix/related-verb-array' into rel/10.4.9-candidate (d5147ed6)
+- fix(graph): the verb fast paths honour every requested type, source, and target (6a89adc4)
+- perf(open): pending-embed recovery is bounded by a low-water mark and runs behind the doors (88e79729)
+- fix(find): connected finds are graph-first — neighbours, then the filter over those ids, then the page (077cbc0b)
+- fix(storage): counts persistence is single-flight, coalesced, and never races its own temp file (5e3b343a)
+
+
+### [10.4.6](https://source.soulcraft.com/soulcraftlabs/open-brainy/compare/v10.4.5...v10.4.6) (2026-08-31)
+
+- fix(transact): metadata-index ops take their JSON-safe view at the crossing, not at construction (73500e7d)
+
+
+### [10.4.5](https://source.soulcraft.com/soulcraftlabs/open-brainy/compare/v10.4.4...v10.4.5) (2026-08-31)
+
+- build(release): the docs-push step retires — this engine documents itself in its own repository (d6bcb14f)
+- fix(generations): a sealed segment may only declare the generations it holds (a963a744)
+- fix(recovery): a torn generation-log tail is a terminal verdict, never a wait (c9930871)
+
+
 ### [10.4.4](https://source.soulcraft.com/soulcraftlabs/open-brainy/compare/v10.4.3...v10.4.4) (2026-08-28)
 
 - fix(vfs): the old-root sweep narrates only when it has something to say (d49148e1)

CONTRIBUTING.md

@@ -41,6 +41,20 @@ npm test
 Tests run on [Vitest](https://vitest.dev/). `npm test` runs the unit suite;
 see `package.json` for `test:integration`, `test:coverage`, and friends.
 
+## Test gate
+
+The release gate is a bare `vitest run` (no `--config` flag) — the same
+command the delta gate and CI's checks invoke. It carries the full
+correctness suite and nothing else: wall-clock/scale benchmarks
+(`tests/performance/**`, `tests/critical-performance-benchmark.test.ts`,
+`tests/api/performance-benchmarks.test.ts`) and the two tests whose outcome
+depends on the host machine or network rather than the code
+(`tests/package-size-limit.test.ts` shells out to the `npm` CLI;
+`tests/model-loading.test.ts` makes a real network call to download a model)
+are excluded from it, because a timing threshold or a flaky network call has
+no business failing a correctness check. That whole family runs on demand,
+in its own exclusive slot, via `npm run test:perf`.
+
 ## Standards
 
 - **Strict TypeScript.** No `any` escape hatches to dodge the type checker.

docs/api-contract.json

@@ -161,6 +161,11 @@
       "kind": "method",
       "arity": 1
     },
+    {
+      "name": "captureEmbedCheckpoint",
+      "kind": "method",
+      "arity": 0
+    },
     {
       "name": "checkHealth",
       "kind": "method",
@@ -225,6 +230,11 @@
       "name": "counts",
       "kind": "accessor"
     },
+    {
+      "name": "createGenerationStore",
+      "kind": "method",
+      "arity": 1
+    },
     {
       "name": "createIndex",
       "kind": "method",
@@ -258,6 +268,11 @@
       "kind": "method",
       "arity": 1
     },
+    {
+      "name": "demoteTornEntityTreeStamp",
+      "kind": "method",
+      "arity": 4
+    },
     {
       "name": "detectIdKind",
       "kind": "method",
@@ -353,11 +368,6 @@
       "kind": "method",
       "arity": 1
     },
-    {
-      "name": "executeGraphSearch",
-      "kind": "method",
-      "arity": 2
-    },
     {
       "name": "executeProximitySearch",
       "kind": "method",
@@ -368,11 +378,21 @@
       "kind": "method",
       "arity": 2
     },
+    {
+      "name": "executeTextSearchScored",
+      "kind": "method",
+      "arity": 3
+    },
     {
       "name": "executeVectorSearch",
       "kind": "method",
       "arity": 3
     },
+    {
+      "name": "executeVectorSearchScored",
+      "kind": "method",
+      "arity": 3
+    },
     {
       "name": "explain",
       "kind": "method",
@@ -418,6 +438,11 @@
       "kind": "method",
       "arity": 2
     },
+    {
+      "name": "filterIdsWithinBelted",
+      "kind": "method",
+      "arity": 2
+    },
     {
       "name": "find",
       "kind": "method",
@@ -711,6 +736,11 @@
       "kind": "method",
       "arity": 2
     },
+    {
+      "name": "hydrateResultPage",
+      "kind": "method",
+      "arity": 2
+    },
     {
       "name": "import",
       "kind": "method",
@@ -741,6 +771,14 @@
       "kind": "method",
       "arity": 0
     },
+    {
+      "name": "isClosed",
+      "kind": "accessor"
+    },
+    {
+      "name": "isClosing",
+      "kind": "accessor"
+    },
     {
       "name": "isEmbeddingReady",
       "kind": "method",
@@ -799,6 +837,16 @@
       "kind": "method",
       "arity": 1
     },
+    {
+      "name": "maybeWriteEmbedCheckpoint",
+      "kind": "method",
+      "arity": 0
+    },
+    {
+      "name": "maybeWriteEmbedLowWater",
+      "kind": "method",
+      "arity": 0
+    },
     {
       "name": "metadataIndexRetractionOp",
       "kind": "method",
@@ -854,6 +902,11 @@
       "kind": "method",
       "arity": 1
     },
+    {
+      "name": "noteEmbedCheckpointCadence",
+      "kind": "method",
+      "arity": 0
+    },
     {
       "name": "noteWriteForPersistence",
       "kind": "method",
@@ -869,6 +922,11 @@
       "kind": "method",
       "arity": 1
     },
+    {
+      "name": "pageConnectedIds",
+      "kind": "method",
+      "arity": 2
+    },
     {
       "name": "pagination",
       "kind": "accessor"
@@ -893,6 +951,11 @@
       "kind": "method",
       "arity": 0
     },
+    {
+      "name": "pendingResult",
+      "kind": "method",
+      "arity": 2
+    },
     {
       "name": "performInit",
       "kind": "method",
@@ -993,6 +1056,11 @@
       "kind": "method",
       "arity": 2
     },
+    {
+      "name": "readPendingEmbedBound",
+      "kind": "method",
+      "arity": 0
+    },
     {
       "name": "ready",
       "kind": "accessor"
@@ -1112,6 +1180,11 @@
       "kind": "method",
       "arity": 2
     },
+    {
+      "name": "resolveConnectedIds",
+      "kind": "method",
+      "arity": 1
+    },
     {
       "name": "resolveDiffEndpoint",
       "kind": "method",
@@ -1155,7 +1228,7 @@
     {
       "name": "rrfFusion",
       "kind": "method",
-      "arity": 4
+      "arity": 3
     },
     {
       "name": "runAggregationBackfillWalk",
@@ -1275,6 +1348,11 @@
       "kind": "method",
       "arity": 1
     },
+    {
+      "name": "textIdsWithinBelted",
+      "kind": "method",
+      "arity": 2
+    },
     {
       "name": "trackField",
       "kind": "method",
@@ -1413,6 +1491,16 @@
       "name": "wireGraphIdResolver",
       "kind": "method",
       "arity": 0
+    },
+    {
+      "name": "writeEmbedCheckpoint",
+      "kind": "method",
+      "arity": 0
+    },
+    {
+      "name": "writeEmbedLowWater",
+      "kind": "method",
+      "arity": 0
     }
   ],
   "errors": [

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "@soulcraftlabs/brainy",
-  "version": "10.4.4",
+  "version": "10.4.11",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "@soulcraftlabs/brainy",
-      "version": "10.4.4",
+      "version": "10.4.11",
       "license": "MIT",
       "dependencies": {
         "@msgpack/msgpack": "^3.1.2",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@soulcraftlabs/brainy",
-  "version": "10.4.4",
+  "version": "10.4.11",
   "brainyContract": 1,
   "description": "Universal Knowledge Protocol™ - World's first Triple Intelligence database unifying vector, graph, and document search in one API. Stage 3 CANONICAL: 42 nouns × 127 verbs covering 96-97% of all human knowledge.",
   "main": "dist/index.js",
@@ -88,7 +88,7 @@
     "test:watch": "NODE_OPTIONS='--max-old-space-size=8192' vitest --config tests/configs/vitest.unit.config.ts",
     "test:coverage": "NODE_OPTIONS='--max-old-space-size=8192' vitest run --config tests/configs/vitest.unit.config.ts --coverage",
     "test:unit": "NODE_OPTIONS='--max-old-space-size=8192' vitest run --config tests/configs/vitest.unit.config.ts",
-    "test:perf": "vitest run tests/unit/performance --reporter=basic",
+    "test:perf": "vitest run --config tests/configs/vitest.perf.config.ts",
     "test:integration": "NODE_OPTIONS='--max-old-space-size=8192' vitest run --config tests/configs/vitest.integration.config.ts",
     "test:semantic": "NODE_OPTIONS='--max-old-space-size=8192' vitest run --config tests/configs/vitest.semantic.config.ts",
     "test:all": "npm run test:unit && npm run test:integration",

scripts/release.sh

@@ -248,17 +248,12 @@ else
   echo -e "${RED}⚠️  FORGEJO_RELEASE_TOKEN unset — no release page created; tag + CHANGELOG remain the record${NC}\n"
 fi
 
-# Step 12: Push public docs to the soulcraft.com docs ingest door
-# (VENUE-DOCS-RELEASE-PUSH). Skips with a loud warning when
-# DOCS_INGEST_SECRET is unset; fails loudly (without undoing the publish —
-# that already happened) when a push errors, so the docs site never
-# silently trails npm.
-echo -e "${BLUE}1️⃣2️⃣ Pushing public docs to soulcraft.com/docs...${NC}"
-if node scripts/push-docs.js; then
-  echo -e "${GREEN}✅ Docs push step done${NC}\n"
-else
-  echo -e "${RED}❌ Docs push FAILED — soulcraft.com/docs trails npm until re-run or interim sync${NC}\n"
-fi
+# Step 12 RETIRED (2026-08-31, CORTEX-SITE-BRAINY-RENAME round 12, David-ruled):
+# soulcraft.com/docs carries the paid product's documentation only. This
+# engine's documentation home is THIS repository — README and docs/ — and the
+# site serves 301s for the slugs this rail used to push. The push script stays
+# in the tree for history; the rail no longer calls it.
+echo -e "${BLUE}Docs step: this engine documents itself in its own repo (site push retired 2026-08-31)${NC}"
 
 echo -e "${GREEN}━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━${NC}"
 echo -e "${GREEN}🎉 Release ${NEW_VERSION} complete!${NC}"

src/db/errors.ts

@@ -351,3 +351,63 @@ export class PendingFlushDurabilityError extends Error {
     this.failedAttempts = failedAttempts
   }
 }
+
+/**
+ * @description Thrown by {@link GenerationStore.commitTransaction} when the
+ * PENDING single-op tier is non-empty — i.e. one or more `commitSingleOp()`
+ * generations are buffered in memory, not yet flushed to
+ * `committedRanges` via `flushPendingSingleOps()`.
+ *
+ * The invariant `reservedGensAsc()` (and everything built on it —
+ * `resolveManyAt`, `resolveAt`, `changedBetween`, the hot-tail window) relies
+ * on is documented, not enforced by types: pending generations must always be
+ * numerically greater than every committed one, because the ONLY sanctioned
+ * callers of `commitTransaction()` — `Brainy.transact()` and
+ * `Brainy.compactHistory()` — flush the pending tier FIRST. A caller that
+ * invokes `commitTransaction()` directly while single-ops are still pending
+ * breaks that invariant: the new commit lands in `committedRanges` ABOVE
+ * generations still sitting in `pendingGens`, so the committed-then-pending
+ * concatenation `reservedGensAsc()` yields is no longer ascending. The
+ * concrete failure this produces is silent, not a crash: `resolveManyAt`
+ * walks committed ranges before pending ones, so it can report a NEWER
+ * generation as the "first after" a pin than an older, still-pending one that
+ * actually touched the id first — a wrong before-image at a point-in-time
+ * read, without a compensating error to warn a caller anything went wrong.
+ *
+ * This error refuses the commit outright, before any staging I/O: nothing is
+ * written, the generation counter reservation is untouched, and
+ * `committedRanges`/`pendingGens` are exactly as they were. Call
+ * `flushPendingSingleOps()` first (or go through `Brainy.transact()`, which
+ * already does).
+ *
+ * @example
+ * try {
+ *   await generationStore.commitTransaction({ touched, execute })
+ * } catch (err) {
+ *   if (err instanceof PendingSingleOpsUnflushedError) {
+ *     await generationStore.flushPendingSingleOps()
+ *     await generationStore.commitTransaction({ touched, execute }) // now safe
+ *   }
+ * }
+ */
+export class PendingSingleOpsUnflushedError extends Error {
+  /** How many un-flushed single-op generations were buffered at refusal time. */
+  public readonly pendingCount: number
+
+  /**
+   * @param pendingCount - `pendingGens.length` at the moment of refusal (always ≥ 1).
+   */
+  constructor(pendingCount: number) {
+    super(
+      `commitTransaction() refused: ${pendingCount} pending single-op generation(s) ` +
+        `are still buffered and un-flushed. Flush the pending single-op tier before ` +
+        `committing a transaction — Brainy.transact() does this automatically; a ` +
+        `direct commitTransaction() call with pending generations would leave the ` +
+        `generation order unsorted (committed generations landing above lower, ` +
+        `still-pending ones) and make point-in-time reads (resolveManyAt/resolveAt) ` +
+        `return the wrong before-image. Call flushPendingSingleOps() first, then retry.`
+    )
+    this.name = 'PendingSingleOpsUnflushedError'
+    this.pendingCount = pendingCount
+  }
+}

src/db/factLog.ts

@@ -40,7 +40,10 @@
  * The manifest (`_generations/facts/manifest.json`, JSON — forensics stay
  * terminal-readable) is the single source of truth for the segment SET;
  * rotation flips it atomically (write-new → fsync → rename) BEFORE the new
- * tail's first byte exists, so no segment file is ever unaccounted for.
+ * tail's first byte exists, so no segment file is ever unaccounted for. Its
+ * per-segment `firstGeneration`/`lastGeneration` are LOAD-BEARING at open: a
+ * recovery pass looking for facts above a bound reads only the segments those
+ * bounds cannot rule out (the prune law — see `segmentsHoldingFactsAbove`).
  *
  * ## Mixed-version logs (the v2 live-write cutover)
  *
@@ -689,6 +692,74 @@ function parseSegment(
   return { facts, validBytes: offset, formatVersion: FACT_LOG_FORMAT_V1 }
 }
 
+/**
+ * THE PRUNE LAW — which segment files a pass looking for facts ABOVE
+ * `committedGeneration` actually has to read, and how many the manifest's own
+ * recorded bounds took off the table.
+ *
+ * A sealed segment's `lastGeneration` is written at SEAL time and never
+ * mutated upward afterwards ({@link FactLog.rotate}, unchanged since the log
+ * was introduced): the tail's bytes are fsynced FIRST (`await this.sync()` —
+ * "sealed segments are always fully durable"), the entry is then built from
+ * the content that fsync covered, and only then does the manifest flip —
+ * atomically (tmp+rename) and fsynced — which in the SAME write re-points
+ * `tailSegment` at a new file, so the sealed file is never appended to again.
+ * A crash anywhere in that order is safe in the pruning direction: crash
+ * before the manifest write and the segment is still the TAIL (read whole);
+ * crash after it and the entry describes bytes that were already durable. The
+ * only later mutation of a sealed segment is `open()`'s straddle truncation,
+ * which REMOVES facts and re-derives the entry from the actual bytes — so a
+ * recorded bound can drift DOWN with its file, never up.
+ *
+ * Therefore: `lastGeneration = L` proves the file holds no fact above L, and
+ * a pass above `committedGeneration >= L` can skip it whole — no read, no
+ * CRC decode, no msgpack. What the manifest cannot PROVE is never pruned: an
+ * entry with no numeric `lastGeneration` (a legacy or hand-repaired manifest)
+ * is read, and the unsealed tail is always read.
+ *
+ * This is the difference between an open that costs O(whole fact log) and one
+ * that costs O(the facts that could matter). MEASURED in production: a 16k-row
+ * brain at generation ~478,819 paid 34-37s of segment reads and CRC decoding
+ * in `generation-store-open-fold` on EVERY open — to answer a question whose
+ * answer, after a clean close, is always "nothing".
+ */
+function segmentsHoldingFactsAbove(
+  stored: FactsManifest,
+  committedGeneration: number
+): { files: string[]; pruned: number } {
+  const files: string[] = []
+  let pruned = 0
+  for (const entry of stored.segments) {
+    const last = (entry as Partial<SegmentEntry>).lastGeneration
+    if (typeof last === 'number' && Number.isFinite(last) && last <= committedGeneration) {
+      pruned++
+      continue
+    }
+    files.push(entry.file)
+  }
+  if (stored.tailSegment) files.push(stored.tailSegment)
+  return { files, pruned }
+}
+
+/**
+ * Say what the open actually read. One line, and only when the log holds more
+ * than one segment (a single-segment log has nothing to prune and nothing to
+ * report) — the operator's receipt that the open is paying for the tail, not
+ * for the whole history.
+ */
+function narrateAboveScan(
+  pass: string,
+  committedGeneration: number,
+  read: number,
+  pruned: number
+): void {
+  if (read + pruned <= 1) return
+  prodLog.narrate(
+    `[FactLog] ${pass} above generation ${committedGeneration}: ${read} segment(s) read, ` +
+      `${pruned} pruned of ${read + pruned} (sealed at or below the bound)`
+  )
+}
+
 /**
  * The generation fact log. One instance per open store; every method assumes
  * the single-writer discipline the generation store already enforces (calls
@@ -754,22 +825,6 @@ export class FactLog {
     return this.manifest.brainId !== undefined || this.tailVersion === FACT_LOG_FORMAT_V2
   }
 
-  /**
-   * Open the log and reconcile it to committed truth: read the manifest,
-   * establish the tail's intact content (torn-tail scan), then TRUNCATE any
-   * fact with `generation > committedGeneration` — those never committed (a
-   * crash between fact-append and the commit point). After open, the log is
-   * exactly the committed prefix.
-   */
-  /**
-   * Read (without truncating) every intact fact ABOVE a generation — the
-   * log-authority recovery surface: after a crash, facts beyond the
-   * manifest watermark that survived with valid CRCs are ACKED writes in
-   * durable-at-ack mode, and the owner REPLAYS them instead of letting
-   * open() truncate them. Must be called BEFORE open() (it reads the raw
-   * segments directly; the torn tail's invalid suffix is ignored exactly
-   * like open() would).
-   */
   /**
    * STREAMING twin of {@link FactLog.peekFactsAbove} for the recovery fold:
    * yields facts above the bound one SEGMENT at a time, ascending, without
@@ -779,13 +834,18 @@ export class FactLog {
    * Works manifest-direct (safe before {@link FactLog.open}). Ordering is
    * structural (segments rotate in order; appends are ordered within one) and
    * ASSERTED — a violation aborts loudly, never a silent misordered replay.
+   *
+   * Reads only the segments that CAN hold a fact above the bound — see
+   * {@link segmentsHoldingFactsAbove}. A bounded fold above a high checkpoint
+   * therefore reads its own tail, not the whole history it already proved
+   * durable.
    */
   async *streamFactsAbove(committedGeneration: number): AsyncGenerator<CommitFact[], void> {
     const stored = (await this.storage.readRawObject(FACTS_MANIFEST_PATH)) as FactsManifest | null
     if (!stored || typeof stored !== 'object' || !Array.isArray(stored.segments)) return
     if (stored.formatVersion !== FACTS_FORMAT_VERSION) return
-    const files = [...stored.segments.map((s) => s.file)]
-    if (stored.tailSegment) files.push(stored.tailSegment)
+    const { files, pruned } = segmentsHoldingFactsAbove(stored, committedGeneration)
+    narrateAboveScan('recovery fold', committedGeneration, files.length, pruned)
     let lastGen = committedGeneration
     for (const file of files) {
       const bytes = await this.storage.readRawBytes(`${FACTS_PREFIX}/${file}`)
@@ -807,13 +867,27 @@ export class FactLog {
     }
   }
 
+  /**
+   * Read (without truncating) every intact fact ABOVE a generation — the
+   * log-authority recovery surface: after a crash, facts beyond the
+   * manifest watermark that survived with valid CRCs are ACKED writes in
+   * durable-at-ack mode, and the owner REPLAYS them instead of letting
+   * open() truncate them. Must be called BEFORE open() (it reads the raw
+   * segments directly; the torn tail's invalid suffix is ignored exactly
+   * like open() would).
+   *
+   * Reads only the segments that CAN hold such a fact — see
+   * {@link segmentsHoldingFactsAbove}. This runs on EVERY log-authority open,
+   * including the clean one where the answer is always empty, so the segments
+   * the manifest already proves irrelevant are never opened at all.
+   */
   async peekFactsAbove(committedGeneration: number): Promise<CommitFact[]> {
     const stored = (await this.storage.readRawObject(FACTS_MANIFEST_PATH)) as FactsManifest | null
     if (!stored || typeof stored !== 'object' || !Array.isArray(stored.segments)) return []
     if (stored.formatVersion !== FACTS_FORMAT_VERSION) return []
     const out: CommitFact[] = []
-    const files = [...stored.segments.map((s) => s.file)]
-    if (stored.tailSegment) files.push(stored.tailSegment)
+    const { files, pruned } = segmentsHoldingFactsAbove(stored, committedGeneration)
+    narrateAboveScan('above-manifest peek', committedGeneration, files.length, pruned)
     for (const file of files) {
       const bytes = await this.storage.readRawBytes(`${FACTS_PREFIX}/${file}`)
       if (bytes === null) continue
@@ -826,6 +900,13 @@ export class FactLog {
     return out
   }
 
+  /**
+   * Open the log and reconcile it to committed truth: read the manifest,
+   * establish the tail's intact content (torn-tail scan), then TRUNCATE any
+   * fact with `generation > committedGeneration` — those never committed (a
+   * crash between fact-append and the commit point). After open, the log is
+   * exactly the committed prefix.
+   */
   async open(committedGeneration: number): Promise<void> {
     const stored = (await this.storage.readRawObject(FACTS_MANIFEST_PATH)) as FactsManifest | null
     if (stored && typeof stored === 'object' && Array.isArray(stored.segments)) {

src/db/familyStamp.ts

@@ -12,9 +12,11 @@
  *   the verified surface is a small set of rollup invariants (entity/
  *   relationship counts) plus `sourceGeneration`.
  *
- * `sourceGeneration` is the generation of the source-of-truth log this
- * projection reflects — open-time coherence becomes a COMPARISON (stamp vs
- * log head), not a walk:
+ * `sourceGeneration` is the COMMITTED generation of the source-of-truth log
+ * this projection reflects — never the allocated counter, which names a
+ * generation that may never commit (see {@link StampVerdict.torn}) — so
+ * open-time coherence becomes a COMPARISON (stamp vs committed head), not a
+ * walk:
  *
  * - equal + invariants hold → coherent, serve.
  * - behind → the projection missed the tail (crash between commit and stamp);
@@ -24,6 +26,9 @@
  * - invariants FAIL at equal generation → genuine incoherence: loud, and the
  *   repair ritual (`repairIndex()`, whose recount rebuilds the rollups from a
  *   canonical walk) heals it.
+ * - AHEAD → a torn generation-log tail: the stamp's fsync outlived the log
+ *   tail's. TERMINAL, never a wait — the generation the stamp names does not
+ *   exist to arrive.
  *
  * Stamps are JSON on purpose — every incident gets debugged by reading a
  * stamp in a terminal.
@@ -70,6 +75,12 @@ export type StampVerdict =
   | { state: 'coherent' }
   | { state: 'absent' } // legacy store — first stamp writes at the next flush
   | { state: 'behind'; stampSource: number; head: number }
+  /**
+   * TORN GENERATION-LOG TAIL: the stamp witnesses a source generation the
+   * store's committed watermark can no longer show. TERMINAL — there is no
+   * generation to wait for, so the open demotes (or refuses) and never spins.
+   */
+  | { state: 'torn'; stampSource: number; head: number }
   | { state: 'incoherent'; failures: string[] }
   | { state: 'unverifiable'; reason: string } // a FAULT reading the stamp — never conflated with absence
 
@@ -118,12 +129,15 @@ export function verifyFamilyStamp(
 ): StampVerdict {
   if (stamp === null) return { state: 'absent' }
   if (stamp.sourceGeneration > head) {
-    // A stamp AHEAD of the log claims state that never committed — the
-    // projection was stamped against truth that a crash rolled back.
-    return {
-      state: 'incoherent',
-      failures: [`sourceGeneration ${stamp.sourceGeneration} is ahead of the log head ${head}`]
-    }
+    // A stamp AHEAD of committed truth witnesses a generation the store can no
+    // longer show: the stamp's fsync survived a crash that the log tail did
+    // not. This is the TORN GENERATION-LOG TAIL — its own class, never folded
+    // in with `incoherent` (a count that drifted at a generation both sides
+    // agree on), because the two have opposite cures: incoherence is recounted,
+    // a tear is DEMOTED. It is also terminal by construction — there is no
+    // generation the open can wait for, because the one the stamp names is
+    // gone.
+    return { state: 'torn', stampSource: stamp.sourceGeneration, head }
   }
   if (stamp.sourceGeneration < head) {
     return { state: 'behind', stampSource: stamp.sourceGeneration, head }

src/db/generationSegments.ts

@@ -147,6 +147,60 @@ export class GenerationSegmentStore {
     return this.coveringSegment(gen) !== null
   }
 
+  /**
+   * @description True when `meta` declares more generations than it holds
+   * frames — a segment sealed by a writer that folded across a hole. The
+   * manifest records `frames` at fold time, so this is an O(1) comparison
+   * against the declared span and needs no I/O.
+   */
+  private isSparse(meta: SegmentMeta): boolean {
+    return meta.lastGeneration - meta.firstGeneration + 1 !== meta.frames
+  }
+
+  /**
+   * @description The generations this tier ACTUALLY holds, as coalesced
+   * ascending intervals — not what the segments declare.
+   *
+   * Dense segments (every one a current writer produces) contribute their
+   * declared range with no I/O. A SPARSE segment — one sealed before the
+   * density law was enforced, whose declared range spans generations it has
+   * no frame for — has its real generation list read from its sidecar and
+   * contributed instead, with the discrepancy narrated once.
+   *
+   * This is what keeps a store that already carries the damage from wedging.
+   * `open()` seeds `committedRanges` from these intervals, so a hole is never
+   * re-admitted as a committed generation, and the auto-compaction pass that
+   * used to fail on every run with "packed history is damaged" simply never
+   * asks for the missing frame.
+   *
+   * @returns Ascending, non-overlapping `[first, last]` intervals.
+   */
+  async actualRanges(): Promise<Array<[number, number]>> {
+    const out: Array<[number, number]> = []
+    for (const meta of this.manifest.segments) {
+      if (!this.isSparse(meta)) {
+        out.push([meta.firstGeneration, meta.lastGeneration])
+        continue
+      }
+      const missing = meta.lastGeneration - meta.firstGeneration + 1 - meta.frames
+      prodLog.warn(
+        `[GenerationSegments] sealed segment ${meta.file} declares generations ` +
+          `${meta.firstGeneration}..${meta.lastGeneration} but holds only ${meta.frames} ` +
+          `frame(s) — ${missing} generation(s) in that span were never folded into it. ` +
+          `Serving the frames it actually holds; the declared span is not treated as ` +
+          `committed history. (Written by a pre-density-law writer that folded across a ` +
+          `gap; the segment itself is intact and no record is lost.)`
+      )
+      const idx = await this.sidecarFor(meta)
+      for (const [gen] of idx.generations) {
+        const last = out[out.length - 1]
+        if (last !== undefined && gen === last[1] + 1) last[1] = gen
+        else out.push([gen, gen])
+      }
+    }
+    return out
+  }
+
   /**
    * Fold consecutive generations into ONE new sealed segment + sidecar and
    * append it to the manifest atomically. Caller guarantees: `gens` is
@@ -164,6 +218,38 @@ export class GenerationSegmentStore {
         throw new Error('[GenerationSegments] fold() input must be strictly ascending')
       }
     }
+    // THE DENSITY LAW, MADE MECHANICAL.
+    //
+    // A sealed segment declares a CONTIGUOUS range [firstGeneration,
+    // lastGeneration] and every reader treats that range as containment:
+    // `coveringSegment` is an interval test, `hasGeneration` returns true for
+    // anything inside it, and `open()` seeds committedRanges from it. So a
+    // segment folded from a SPARSE input silently claims generations it does
+    // not hold, and the first read of one of those holes throws
+    // "inside sealed segment ... but has no frame — packed history is damaged".
+    //
+    // That is exactly how the damage was produced. `repackHistory` skipped
+    // generations mid-batch — ones absent from committedRanges, ones still in
+    // the pending buffer, ones whose tx.json would not read — and handed the
+    // survivors here, where the range was computed from the first and last of
+    // them. Worse, the mis-declared range was then merged back into
+    // committedRanges at the next open, which is what turned a quiet hole into
+    // a repeating auto-compaction failure on every subsequent run.
+    //
+    // Callers now split at discontinuities; this refusal is what keeps any
+    // future caller from reintroducing the class. A refusal here loses
+    // nothing — the generations stay in the live tier, readable, and the next
+    // pass folds them correctly.
+    for (let i = 1; i < gens.length; i++) {
+      if (gens[i].generation !== gens[i - 1].generation + 1) {
+        throw new Error(
+          `[GenerationSegments] fold() input is not contiguous: ${gens[i - 1].generation} → ` +
+            `${gens[i].generation} skips ${gens[i].generation - gens[i - 1].generation - 1} ` +
+            `generation(s). A sealed segment declares a dense range, so folding a sparse ` +
+            `batch would claim generations it does not hold. Split the batch at the gap.`
+        )
+      }
+    }
     const last = this.manifest.segments[this.manifest.segments.length - 1]
     if (last && gens[0].generation <= last.lastGeneration) {
       throw new Error(
@@ -364,12 +450,37 @@ export class GenerationSegmentStore {
         return this.decodeFrame(payload)
       }
     }
-    // In the covering range but not present: the packed tier is dense by
-    // construction (fold packs every generation it is handed, including
-    // record-less ones) — absence inside a sealed range is damage.
+    // Inside the covering range but with no frame. Two very different causes,
+    // and conflating them is what made this class wedge every maintenance pass
+    // on the affected stores.
+    //
+    // (1) A SPARSE SEGMENT — the manifest's own `frames` count is smaller than
+    //     the span it declares. That segment was sealed by a writer that
+    //     folded across a hole (the class this file's density law now bars).
+    //     The segment is INTACT and nothing is lost; it simply never held this
+    //     generation. Answering "not packed" is the honest answer, and it lets
+    //     the caller's two-tier read decide what a genuinely absent generation
+    //     means, instead of every compaction pass dying on a repeating throw.
+    //     `actualRanges()` keeps such holes out of committedRanges at open, so
+    //     in a healed store nobody asks this question in the first place.
+    //
+    // (2) A DENSE SEGMENT missing a frame it says it has — the manifest and
+    //     the sidecar disagree about a segment that claims to be complete.
+    //     That IS damage, and it stays loud.
+    if (this.isSparse(meta)) {
+      prodLog.warn(
+        `[GenerationSegments] generation ${gen} falls inside sealed segment ${meta.file}'s ` +
+          `declared range ${meta.firstGeneration}..${meta.lastGeneration}, but that segment ` +
+          `holds ${meta.frames} frame(s) for a ${meta.lastGeneration - meta.firstGeneration + 1}` +
+          `-generation span — it was sealed across a gap and never held this generation. ` +
+          `Reporting it as unpacked rather than as damage; no record is lost.`
+      )
+      return null
+    }
     throw new Error(
       `[GenerationSegments] generation ${gen} is inside sealed segment ${meta.file}'s declared ` +
-        `range but has no frame — packed history is damaged`
+        `range but has no frame, and that segment declares a complete ${meta.frames}-frame ` +
+        `span — the manifest and the sidecar disagree; packed history is damaged`
     )
   }
 

src/db/generationStore.ts

@@ -32,7 +32,13 @@
  */
 
 import { prodLog } from '../utils/logger.js'
-import { GenerationCompactedError, GenerationConflictError, PendingFlushDurabilityError, StoreInconsistentError } from './errors.js'
+import {
+  GenerationCompactedError,
+  GenerationConflictError,
+  PendingFlushDurabilityError,
+  PendingSingleOpsUnflushedError,
+  StoreInconsistentError
+} from './errors.js'
 import type { UnreconciledRecord } from './errors.js'
 import { TransactionRollbackError } from '../transaction/errors.js'
 import type {
@@ -96,6 +102,35 @@ export const FOLD_CHECKPOINT_PATH = '_system/fold-checkpoint.json'
 /** Storage-root-relative prefix of the per-generation record directories. */
 export const GENERATIONS_PREFIX = '_generations'
 
+/**
+ * @description Split an ascending list of fold candidates into maximal
+ * CONTIGUOUS runs — `[7,8,9,12,13]` becomes `[[7,8,9],[12,13]]`.
+ *
+ * A sealed segment declares one dense range `[firstGeneration,
+ * lastGeneration]`, and every reader treats that range as containment. So a
+ * batch with a hole in it must never become one segment: it would claim a
+ * generation it does not hold, and the first read of that hole reports the
+ * packed history as damaged. One run, one segment — the ranges then describe
+ * exactly what the segments contain.
+ *
+ * @param gens - Fold candidates, strictly ascending by generation.
+ * @returns One array per contiguous run, in ascending order. Empty in, empty out.
+ */
+export function contiguousRuns(gens: FoldGeneration[]): FoldGeneration[][] {
+  const runs: FoldGeneration[][] = []
+  let run: FoldGeneration[] = []
+  for (const g of gens) {
+    const prev = run[run.length - 1]
+    if (prev !== undefined && g.generation !== prev.generation + 1) {
+      runs.push(run)
+      run = []
+    }
+    run.push(g)
+  }
+  if (run.length > 0) runs.push(run)
+  return runs
+}
+
 /**
  * @description Phases of the {@link GenerationStore.commitTransaction} commit
  * protocol at which a test-only fault injector can simulate a process crash.
@@ -770,7 +805,16 @@ export class GenerationStore {
         if (uncleanOpen) await this.advanceFoldCheckpointUnlocked()
         // The marker is consumed: any session that can write invalidates it
         // at first commit (see the commit paths); a clean close re-writes it.
-        await this.clearCleanShutdownMarker()
+        // A READER NEVER CONSUMES IT. The marker is the writer's own evidence
+        // about the writer's own process — clearing it here exists so that
+        // if THIS session goes on to write and then dies before its next
+        // clean close, the marker's absence correctly reads as unclean. A
+        // reader can never write, so it can never leave the store in a state
+        // its own crash would mis-describe; clearing the marker for it would
+        // only cost the store's actual writer a needless whole-log fold on
+        // its next open, for a generation the reader merely observed. Leave
+        // `_system/` exactly as found.
+        if (!options?.readOnly) await this.clearCleanShutdownMarker()
       }
       await this.factLog.open(this.committed)
     } else {
@@ -784,9 +828,15 @@ export class GenerationStore {
     if (storageSupportsFactLog(this.storage)) {
       this.segments = new GenerationSegmentStore(this.storage)
       await this.segments.open()
-      const packedRanges = this.segments
-        .segments()
-        .map((s): [number, number] => [s.firstGeneration, Math.min(s.lastGeneration, this.committed)])
+      // ACTUAL ranges, not declared ones. A segment sealed by a pre-density-law
+      // writer can declare a span wider than the frames it holds; seeding
+      // committedRanges from the declared span re-admits those holes as
+      // committed generations, and every later maintenance pass then asks for a
+      // frame that was never written. `actualRanges()` reads the real
+      // generation list from the sidecar for exactly those segments (and does
+      // no I/O for the dense ones, which is all of them on a healthy store).
+      const packedRanges = (await this.segments.actualRanges())
+        .map((r): [number, number] => [r[0], Math.min(r[1], this.committed)])
         .filter(([lo, hi]) => lo <= hi)
       if (packedRanges.length > 0) {
         // Merge packed (older) + live (newer) interval sets — both ascending;
@@ -854,7 +904,11 @@ export class GenerationStore {
     }
   }
 
-  /** Consume the clean-shutdown marker (every open; a clean close re-writes it). */
+  /**
+   * Consume the clean-shutdown marker (every WRITER open; a clean close
+   * re-writes it). Callers must gate this on `!options.readOnly` — a reader
+   * never consumes the marker, see the call site in {@link open}.
+   */
   private async clearCleanShutdownMarker(): Promise<void> {
     try {
       await this.storage.deleteRawObject(CLEAN_SHUTDOWN_PATH)
@@ -1316,6 +1370,9 @@ export class GenerationStore {
    * @param args.execute - Runs the planned operation batch atomically.
    * @returns The committed generation and its commit timestamp.
    * @throws GenerationConflictError when the CAS expectation fails.
+   * @throws PendingSingleOpsUnflushedError when the pending single-op tier is
+   *   non-empty — call `flushPendingSingleOps()` first (both `Brainy.transact()`
+   *   and `Brainy.compactHistory()` already do).
    */
   /**
    * The generation fact log, or `null` when the storage layer cannot host one.
@@ -1390,6 +1447,13 @@ export class GenerationStore {
     execute: () => Promise<void>
   }): Promise<{ generation: number; timestamp: number }> {
     return this.withMutex(async () => {
+      // The generation-order guard (see assertPendingSingleOpsFlushed): a
+      // direct commitTransaction() call while single-ops are still pending
+      // would commit above them, unsorting reservedGensAsc() and corrupting
+      // point-in-time reads. Both sanctioned callers (Brainy.transact(),
+      // Brainy.compactHistory()) already flush first, so this is
+      // behavior-neutral on every real path.
+      this.assertPendingSingleOpsFlushed()
       // A latched history-durability failure compromises the whole generation
       // chain — refuse a transact too (advancing the manifest past stuck,
       // un-durable single-op generations would be inconsistent). Same loud
@@ -2259,6 +2323,37 @@ export class GenerationStore {
     }
   }
 
+  /**
+   * @description Throw if the pending single-op tier is non-empty. Called at
+   * the top of {@link commitTransaction} (the ONLY method that appends a
+   * fresh commit directly into {@link committedRanges} outside recovery) so
+   * the ordering invariant {@link reservedGensAsc}'s own doc comment states —
+   * "pending generations are always greater than every committed one" — is
+   * ENFORCED there rather than merely assumed.
+   *
+   * That invariant holds today only because both sanctioned callers flush the
+   * pending tier before committing: `Brainy.transact()` (src/brainy.ts,
+   * `await this.generationStore.flushPendingSingleOps()` immediately before
+   * its `commitTransaction()` call) and `Brainy.compactHistory()`
+   * (src/brainy.ts, the same flush immediately before its `compact()` call —
+   * `compact()` itself only ever RECLAIMS an existing committed prefix, so it
+   * cannot land a commit out of order and needs no guard of its own). A
+   * caller that reaches `commitTransaction()` by any other path — bypassing
+   * that flush — would commit a new generation into `committedRanges` ABOVE
+   * generations still sitting in `pendingGens`, breaking `reservedGensAsc`'s
+   * "committed-then-pending is already sorted" assumption and making
+   * `resolveManyAt`'s single ascending pass (and `resolveAt`'s consumers)
+   * return the WRONG before-image for a point-in-time read — silently, no
+   * compensating error. Refusing here, before any staging I/O, keeps the
+   * store untouched (nothing committed, nothing staged, the generation
+   * counter reservation unaffected) on every path that already flushes.
+   */
+  private assertPendingSingleOpsFlushed(): void {
+    if (this.pendingGens.length > 0) {
+      throw new PendingSingleOpsUnflushedError(this.pendingGens.length)
+    }
+  }
+
   /** Schedule a coalesced pending-tier flush (size trigger fires immediately on
    *  the next microtask; otherwise a {@link PENDING_FLUSH_DELAY_MS} timer). Both
    *  defer outside the current mutex section so the flush can re-acquire it. A
@@ -2342,6 +2437,13 @@ export class GenerationStore {
    * committed-then-pending concatenation is already sorted — identical to the old
    * `[...committedGens, ...pendingGens]`. This is the union historical reads
    * resolve over so un-flushed single-ops are visible to pins/`asOf`.
+   *
+   * The "flush first" half of that invariant is ENFORCED, not just documented:
+   * {@link commitTransaction} — the only method that lands a fresh commit into
+   * {@link committedRanges} outside crash recovery — refuses via
+   * {@link assertPendingSingleOpsFlushed} whenever {@link pendingGens} is
+   * non-empty, so a committed generation can never land above a still-pending
+   * one and break this ordering.
    */
   private *reservedGensAsc(): IterableIterator<number> {
     yield* this.committedGensAsc()
@@ -3121,13 +3223,26 @@ export class GenerationStore {
           foldInput.push({ generation: gen, timestamp: delta.timestamp, delta, records })
         }
         if (foldInput.length === 0) continue
-        await segments.fold(foldInput)
-        segmentsCreated++
-        // Segment + manifest durable → the live copies retire.
-        for (const g of foldInput) {
-          await this.storage.removeRawPrefix(`${GENERATIONS_PREFIX}/${g.generation}`)
+        // SPLIT AT DISCONTINUITIES. `eligible` is NOT contiguous — three
+        // filters above punch holes in it: a generation missing from
+        // committedRanges never appears, one still in the pending buffer is
+        // skipped, and one whose tx.json will not read is skipped. A sealed
+        // segment declares a DENSE range, so folding across such a hole makes
+        // the segment claim a generation it does not hold; the next open
+        // merges that mis-declared range into committedRanges, and every
+        // subsequent auto-compaction pass then asks for the missing frame and
+        // fails with "packed history is damaged". Fold each contiguous RUN as
+        // its own segment instead — same bytes, honest ranges.
+        for (const run of contiguousRuns(foldInput)) {
+          if (deadline !== undefined && Date.now() >= deadline) break
+          await segments.fold(run)
+          segmentsCreated++
+          // Segment + manifest durable → the live copies retire.
+          for (const g of run) {
+            await this.storage.removeRawPrefix(`${GENERATIONS_PREFIX}/${g.generation}`)
+          }
+          folded += run.length
         }
-        folded += foldInput.length
       }
       if (folded > 0) {
         prodLog.info(

src/index.ts

@@ -231,7 +231,8 @@ export {
   GenerationCompactedError,
   StoreInconsistentError,
   PendingFlushDurabilityError,
-  CanonicalEnumerationUnavailableError
+  CanonicalEnumerationUnavailableError,
+  PendingSingleOpsUnflushedError
 } from './db/errors.js'
 export type { UnreconciledRecord } from './db/errors.js'
 export type {

src/neural/embeddedTypeEmbeddings.ts

@@ -2,7 +2,7 @@
  * 🧠 BRAINY EMBEDDED TYPE EMBEDDINGS
  *
  * AUTO-GENERATED - DO NOT EDIT
- * Generated: 2026-06-29T10:04:19-07:00
+ * Generated: 2026-08-27T09:18:45-07:00
  * Noun Types: 42
  * Verb Types: 127
  *
@@ -19,7 +19,7 @@ export const TYPE_METADATA = {
   verbTypes: 127,
   totalTypes: 169,
   embeddingDimensions: 384,
-  generatedAt: "2026-06-29T10:04:19-07:00",
+  generatedAt: "2026-08-27T09:18:45-07:00",
   sizeBytes: {
     embeddings: 259584,
     base64: 346112

src/plugin.ts

@@ -411,7 +411,90 @@ export interface MetadataIndexProvider {
    * @returns The matching id universe as an opaque set.
    */
   getIdSetForFilter?(filter: any): Promise<OpaqueIdSet>
+  /**
+   * @description OPTIONAL: evaluate `filter` over `ids` ONLY and return the
+   * survivors in the caller's order — the door a graph-first
+   * `find({ connected, where })` walks. The neighbour set is the universe there,
+   * so the filter must cost O(|ids|) membership checks, never a whole-store
+   * materialization. A native index answers from its roaring filter result
+   * (membership by entity int); the reference index answers from its own
+   * `getIdsForFilter`, so the two doors can never disagree. Absent → Brainy
+   * intersects `getIdsForFilter`'s answer with `ids` itself (correct, O(store)).
+   * @param filter - The same filter shape accepted by `getIdsForFilter`.
+   * @param ids - The candidate ids (canonical). The answer is a subsequence.
+   */
+  filterIdsWithin?(filter: any, ids: readonly string[]): Promise<string[]>
+  /**
+   * @description OPTIONAL: plan and execute a WHOLE `find()` — the graph
+   * traversal, the metadata filter, the ordering and the page — and answer the
+   * page's ids, or `null` for a shape this index does not plan.
+   *
+   * The doors above each serve one stage, so a `find()` that consults three of
+   * them crosses into the index three times and marshals a result set at every
+   * crossing. An index that can decide the stage ORDER itself does the whole
+   * thing in one call and materializes ids only for the page — a filter
+   * matching a hundred thousand rows then builds twenty-five id strings instead
+   * of a hundred thousand.
+   *
+   * The contract this door must keep, because Brainy cannot check it:
+   *
+   * - **The same answer.** Identical rows, in identical order, to what the
+   *   stage doors would have produced for the same params. This door changes
+   *   which code runs, never what the answer is.
+   * - **The law of the stages** (`find({ connected })` is graph-first): the
+   *   neighbour set is the candidate universe, the filter is evaluated over
+   *   those ids only, `orderBy` sorts the whole candidate set, and the page is
+   *   cut LAST.
+   * - **`null` before work, not instead of an answer.** A shape the index does
+   *   not plan must be handed back BEFORE any evaluation, so Brainy serves it
+   *   through the stage doors exactly as it always has. Returning `null` after
+   *   partial work, or an empty page for a shape it could not evaluate, is a
+   *   silent wrong answer.
+   * - **`emptyAt` names the stage** that produced an empty page — `'graph'`,
+   *   `'filter'`, `'visibility'` or `'none'` — so Brainy can apply its serving
+   *   law to the right index. An empty answer from an index that is not
+   *   serving must refuse loudly, and Brainy can only re-verify what it is told.
+   *
+   * Absent → every `find()` is served by the stage doors, which is Brainy's
+   * own behaviour and the ordering oracle for any implementation of this one.
+   * @param params - The find params, already normalized by `find()`
+   *   (natural-language parsed, `connected` anchors resolved to canonical ids,
+   *   an empty `where` dropped).
+   * @param hiddenIds - Ids this read must not return. The contract is the ANSWER, not the
+   *   mechanism: a provider may subtract this set before paging, or derive the
+   *   same exclusion from the params' visibility tiers itself — either way the
+   *   page must equal the engine's own answer with none of these ids in it.
+   * @param graphIndex - The active graph provider, for a `connected` plan.
+   * @returns The page's ids plus the stage that emptied it, or `null`.
+   */
+  planFindPage?(
+    params: any,
+    hiddenIds: readonly string[],
+    graphIndex: unknown
+  ): Promise<{ ids: string[]; emptyAt: 'graph' | 'filter' | 'visibility' | 'none' } | null>
   getIdsForTextQuery(query: string): Promise<Array<{ id: string; matchCount: number }>>
+  /**
+   * @description OPTIONAL: score `query` over `ids` ONLY — the text-leg twin of
+   * {@link filterIdsWithin}, and the door a hybrid `find({ query, where })`
+   * walks. The metadata filter's universe is the candidate set there, so the
+   * text leg must cost O(|ids|) membership checks and marshal at most `|ids|`
+   * rows, never the whole posting list of every query word. A native index
+   * intersects its own postings with the candidate set (membership by entity
+   * int) before any string crosses the boundary; the reference index answers
+   * from its own `getIdsForTextQuery`, so the two doors can never disagree.
+   * Absent → Brainy intersects `getIdsForTextQuery`'s answer with `ids` itself
+   * (correct, and still hydrate-last, but it marshals the whole answer).
+   *
+   * The answer keeps `getIdsForTextQuery`'s contract: `{ id, matchCount }`
+   * sorted by `matchCount` descending, ties in the order the whole-store answer
+   * would have produced. Only rows in `ids` may appear.
+   * @param query - The same text query accepted by `getIdsForTextQuery`.
+   * @param ids - The candidate ids (canonical). The answer is a subset.
+   */
+  getIdsForTextQueryWithin?(
+    query: string,
+    ids: readonly string[]
+  ): Promise<Array<{ id: string; matchCount: number }>>
   getSortedIdsForFilter(filter: any, orderBy: string, order?: 'asc' | 'desc', topK?: number): Promise<string[]>
   getFilterValues(field: string): Promise<string[]>
   getFilterFields(): Promise<string[]>

src/storage/adapters/baseStorageAdapter.ts

@@ -1089,6 +1089,10 @@ export abstract class BaseStorageAdapter implements StorageAdapter {
 
   // Counts changed since the last persist? Drives the write-through flush.
   protected pendingCountPersist = false
+  /** The one persist running right now, if any (single-flight law — see flushCounts). */
+  private countPersistInFlight: Promise<void> | null = null
+  /** The one trailing persist a burst has queued behind the in-flight one. */
+  private countPersistTrailing: Promise<void> | null = null
 
   /**
    * Get total noun count - O(1) operation
@@ -1341,15 +1345,46 @@ export abstract class BaseStorageAdapter implements StorageAdapter {
       return
     }
 
-    try {
-      // Persist to storage (implemented by subclass)
-      await this.persistCounts()
-      this.pendingCountPersist = false
-    } catch (error) {
-      console.error('CRITICAL: Failed to flush counts to storage:', error)
-      // Keep pending flag set so we retry on next operation
-      throw error
+    // SINGLE-FLIGHT, COALESCED. Counts are write-through on every change, so
+    // a burst of writes used to launch one persist per change, all in flight
+    // together. Two of them inside the same millisecond shared the atomic
+    // writer's temp path (`.tmp-<pid>-<ms>`): both wrote it, the first rename
+    // consumed it, the second rename found nothing — ENOENT, ~1,500 times a
+    // day on a busy production brain, with a full ledger write per change
+    // behind it. Now exactly one persist runs at a time; requests that arrive
+    // while it runs collapse into ONE trailing persist that carries the final
+    // state. A burst of N changes costs at most two writes and never races
+    // itself.
+    if (this.countPersistInFlight) {
+      // The in-flight write may have already serialised a stale snapshot —
+      // ask for one more pass after it, and let every caller in this burst
+      // await that same pass.
+      if (!this.countPersistTrailing) {
+        this.countPersistTrailing = this.countPersistInFlight
+          .catch(() => undefined)
+          .then(() => {
+            this.countPersistTrailing = null
+            return this.flushCounts()
+          })
+      }
+      return this.countPersistTrailing
     }
+
+    this.countPersistInFlight = (async () => {
+      try {
+        // Persist to storage (implemented by subclass)
+        this.pendingCountPersist = false
+        await this.persistCounts()
+      } catch (error) {
+        // Keep the flag set so the next operation retries.
+        this.pendingCountPersist = true
+        console.error('CRITICAL: Failed to flush counts to storage:', error)
+        throw error
+      } finally {
+        this.countPersistInFlight = null
+      }
+    })()
+    return this.countPersistInFlight
   }
 
   /**

src/storage/adapters/fileSystemStorage.ts

@@ -2400,8 +2400,15 @@ export class FileSystemStorage extends BaseStorage {
    * Atomic write via temp-file-then-rename so concurrent readers never see a
    * half-written lock JSON. Reused by writer-lock writes + heartbeat.
    */
+  /** Monotonic per-process sequence so two atomic writes never share a temp path. */
+  private static atomicWriteSeq = 0
+
   private async writeFileAtomic(filePath: string, contents: string): Promise<void> {
-    const tmp = `${filePath}.tmp-${process.pid}-${Date.now()}`
+    // pid + timestamp alone collided: two writers of the same target inside
+    // one millisecond shared this path, and the loser's rename found the
+    // winner had already moved it (ENOENT). The sequence makes every call's
+    // temp path its own.
+    const tmp = `${filePath}.tmp-${process.pid}-${Date.now()}-${++FileSystemStorage.atomicWriteSeq}`
     await fs.promises.writeFile(tmp, contents)
     await fs.promises.rename(tmp, filePath)
   }

src/storage/baseStorage.ts

@@ -2942,19 +2942,33 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         !options.filter.service &&
         !options.filter.metadata
       ) {
-        const sourceId = Array.isArray(options.filter.sourceId)
-          ? options.filter.sourceId[0]
-          : options.filter.sourceId
+        const sourceIds = Array.isArray(options.filter.sourceId)
+          ? options.filter.sourceId
+          : [options.filter.sourceId]
 
-        const verbType = Array.isArray(options.filter.verbType)
-          ? options.filter.verbType[0]
-          : options.filter.verbType
+        // EVERY requested verb type is honoured — an array used to collapse to
+        // its first element here, silently dropping the rest of the ask.
+        const verbTypes = new Set(
+          Array.isArray(options.filter.verbType)
+            ? options.filter.verbType
+            : [options.filter.verbType]
+        )
 
-        // Get verbs by source, then filter by type (O(1) graph lookup + O(n) type filter),
-        // then apply the subtype / visibility metadata filters on the candidate set.
-        const verbsBySource = await this.getVerbsBySource_internal(sourceId)
+        // Get verbs by source (union over every requested source), filter by the
+        // requested type SET (O(1) graph lookup + O(n) type filter), then apply
+        // the subtype / visibility metadata filters on the candidate set.
+        const bySource: HNSWVerbWithMetadata[] = []
+        const seenVerbIds = new Set<string>()
+        for (const oneSource of sourceIds) {
+          for (const v of await this.getVerbsBySource_internal(oneSource)) {
+            if (!seenVerbIds.has(v.id)) {
+              seenVerbIds.add(v.id)
+              bySource.push(v)
+            }
+          }
+        }
         const filteredVerbs = this.applyVerbMetadataFilters(
-          verbsBySource.filter(v => v.verb === verbType),
+          bySource.filter(v => verbTypes.has(v.verb)),
           options.filter
         )
 
@@ -2985,16 +2999,22 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         !options.filter.service &&
         !options.filter.metadata
       ) {
-        const sourceId = Array.isArray(options.filter.sourceId)
-          ? options.filter.sourceId[0]
-          : options.filter.sourceId
-
-        // Get verbs by source directly (hydrated with metadata), then apply the
-        // subtype / visibility metadata filters on the O(degree) candidate set.
-        const verbsBySource = this.applyVerbMetadataFilters(
-          await this.getVerbsBySource_internal(sourceId),
-          options.filter
-        )
+        // EVERY requested source is honoured — an array used to collapse to
+        // its first element here, silently dropping the rest of the ask.
+        const onlySourceIds = Array.isArray(options.filter.sourceId)
+          ? options.filter.sourceId
+          : [options.filter.sourceId]
+        const sourceUnion: HNSWVerbWithMetadata[] = []
+        const seenSourceVerbIds = new Set<string>()
+        for (const oneSource of onlySourceIds) {
+          for (const v of await this.getVerbsBySource_internal(oneSource)) {
+            if (!seenSourceVerbIds.has(v.id)) {
+              seenSourceVerbIds.add(v.id)
+              sourceUnion.push(v)
+            }
+          }
+        }
+        const verbsBySource = this.applyVerbMetadataFilters(sourceUnion, options.filter)
 
         // Apply pagination
         const paginatedVerbs = verbsBySource.slice(offset, offset + limit)
@@ -3023,16 +3043,22 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         !options.filter.service &&
         !options.filter.metadata
       ) {
-        const targetId = Array.isArray(options.filter.targetId)
-          ? options.filter.targetId[0]
-          : options.filter.targetId
-
-        // Get verbs by target directly (hydrated with metadata), then apply the
-        // subtype / visibility metadata filters on the O(degree) candidate set.
-        const verbsByTarget = this.applyVerbMetadataFilters(
-          await this.getVerbsByTarget_internal(targetId),
-          options.filter
-        )
+        // EVERY requested target is honoured — an array used to collapse to
+        // its first element here, silently dropping the rest of the ask.
+        const onlyTargetIds = Array.isArray(options.filter.targetId)
+          ? options.filter.targetId
+          : [options.filter.targetId]
+        const targetUnion: HNSWVerbWithMetadata[] = []
+        const seenTargetVerbIds = new Set<string>()
+        for (const oneTarget of onlyTargetIds) {
+          for (const v of await this.getVerbsByTarget_internal(oneTarget)) {
+            if (!seenTargetVerbIds.has(v.id)) {
+              seenTargetVerbIds.add(v.id)
+              targetUnion.push(v)
+            }
+          }
+        }
+        const verbsByTarget = this.applyVerbMetadataFilters(targetUnion, options.filter)
 
         // Apply pagination
         const paginatedVerbs = verbsByTarget.slice(offset, offset + limit)
@@ -3061,16 +3087,25 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         !options.filter.service &&
         !options.filter.metadata
       ) {
-        const verbType = Array.isArray(options.filter.verbType)
-          ? options.filter.verbType[0]
-          : options.filter.verbType
+        // EVERY requested verb type is honoured — an array used to collapse to
+        // its first element here, silently dropping the rest of the ask.
+        const verbTypes = Array.isArray(options.filter.verbType)
+          ? options.filter.verbType
+          : [options.filter.verbType]
 
-        // Get verbs by type directly (hydrated with metadata), then apply the
-        // subtype / visibility metadata filters on the candidate set.
-        const verbsByType = this.applyVerbMetadataFilters(
-          await this.getVerbsByType_internal(verbType),
-          options.filter
-        )
+        // Get verbs by each requested type (hydrated with metadata), deduped by
+        // id, then apply the subtype / visibility metadata filters on the set.
+        const byType: HNSWVerbWithMetadata[] = []
+        const seenTypeVerbIds = new Set<string>()
+        for (const oneType of verbTypes) {
+          for (const v of await this.getVerbsByType_internal(oneType)) {
+            if (!seenTypeVerbIds.has(v.id)) {
+              seenTypeVerbIds.add(v.id)
+              byType.push(v)
+            }
+          }
+        }
+        const verbsByType = this.applyVerbMetadataFilters(byType, options.filter)
 
         // Apply pagination
         const paginatedVerbs = verbsByType.slice(offset, offset + limit)

src/transaction/operations/IndexOperations.ts

@@ -14,6 +14,7 @@ import type { MetadataIndexManager } from '../../utils/metadataIndex.js'
 import type { GraphVerb } from '../../coreTypes.js'
 import type { Operation, RollbackAction } from '../types.js'
 import { isZeroNormVector } from '../../utils/distance.js'
+import { jsonSafeIndexMetadata } from '../../utils/jsonSafeIndexMetadata.js'
 import { prodLog } from '../../utils/logger.js'
 
 /**
@@ -390,13 +391,21 @@ export class AddToMetadataIndexOperation implements Operation {
     // rollback so add + undo reference the same watermark.
     const generation = this.generationFn?.()
 
-    // Add to metadata index (skipFlush=true for transaction atomicity)
-    await this.index.addToIndex(this.id, this.entity, true, false, generation)
+    // The JSON-safe view is taken HERE, per crossing, never at construction:
+    // the entity reference this op holds can be mutated between plan and
+    // execute (a graph op's execute-time endpoint-int resolution mirrors
+    // BigInts onto a shared verb object) — see jsonSafeIndexMetadata's
+    // module doc.
+    await this.index.addToIndex(
+      this.id, jsonSafeIndexMetadata(this.entity), true, false, generation
+    )
 
     // Return rollback action
     return async () => {
       // Remove from metadata index
-      await this.index.removeFromIndex(this.id, this.entity, generation)
+      await this.index.removeFromIndex(
+        this.id, jsonSafeIndexMetadata(this.entity), generation
+      )
     }
   }
 }
@@ -432,13 +441,21 @@ export class RemoveFromMetadataIndexOperation implements Operation {
     // Resolve the removal generation once; reuse it for the rollback re-add.
     const generation = this.generationFn?.()
 
-    // Remove from metadata index
-    await this.index.removeFromIndex(this.id, this.entity, generation)
+    // Sanitized per crossing, never at construction — transact()'s delete
+    // legs hand this op the SAME verb object the graph-retraction op's
+    // execute-time endpoint resolution mutates (BigInt sourceInt/targetInt),
+    // so a plan-time view aliases the pollution. See jsonSafeIndexMetadata's
+    // module doc.
+    await this.index.removeFromIndex(
+      this.id, jsonSafeIndexMetadata(this.entity), generation
+    )
 
     // Return rollback action
     return async () => {
       // Re-add with original metadata (skipFlush=true)
-      await this.index.addToIndex(this.id, this.entity, true, false, generation)
+      await this.index.addToIndex(
+        this.id, jsonSafeIndexMetadata(this.entity), true, false, generation
+      )
     }
   }
 }

src/utils/jsonSafeIndexMetadata.ts

@@ -0,0 +1,47 @@
+/**
+ * @module utils/jsonSafeIndexMetadata
+ * @description The metadata-index crossing's JSON-safety law, as a leaf
+ * function both the coordinator and the transaction operations share.
+ *
+ * The seam's metadata is JSON-safe BY CONTRACT (a native provider serializes
+ * it; u64 ints as Number corrupt above 2^53) — but `resolveVerbEndpointInts`
+ * MIRRORS the resolved endpoint ints onto the verb object itself as BigInt
+ * (`verb.sourceInt`/`targetInt`), so a verb object reused as index metadata
+ * carries BigInts into JSON.stringify, which throws, aborting the whole
+ * transaction. Endpoint ints ride their OWN op params on the graph legs — the
+ * metadata crossing drops every BigInt-valued top-level key instead of
+ * guessing at a lossy numeric encoding.
+ *
+ * WHY THIS IS A LEAF MODULE, ENFORCED AT THE CROSSING: sanitizing only at
+ * operation-construction time is not enough. `transact()`'s delete legs pass
+ * the SAME verb object to both the graph-retraction op (whose endpoint-int
+ * thunk deliberately resolves at EXECUTE time, for same-batch forward refs)
+ * and the metadata-retraction op. At plan time the verb is still clean, so a
+ * plan-time sanitize returns the same reference — then the graph op executes
+ * first, mirrors the BigInt ints onto the shared object, and the metadata op
+ * crosses the seam with them (found by the first fleet adoption of the native
+ * pair: every transact-wrapped edge delete aborted). The crossing itself is
+ * the only place ordering cannot bypass.
+ */
+
+/**
+ * A JSON-safe view of a record bound for the metadata-index crossing.
+ *
+ * @param metadata - The candidate index-metadata record.
+ * @returns The same object when already JSON-safe, else a shallow copy
+ *   without the BigInt-valued keys.
+ */
+export function jsonSafeIndexMetadata(metadata: unknown): unknown {
+  if (metadata === null || typeof metadata !== 'object') return metadata
+  const rec = metadata as Record<string, unknown>
+  let hasBigint = false
+  for (const k in rec) {
+    if (typeof rec[k] === 'bigint') { hasBigint = true; break }
+  }
+  if (!hasBigint) return metadata
+  const out: Record<string, unknown> = {}
+  for (const k in rec) {
+    if (typeof rec[k] !== 'bigint') out[k] = rec[k]
+  }
+  return out
+}

src/utils/metadataIndex.ts

@@ -1509,11 +1509,56 @@ export class MetadataIndexManager implements MetadataIndexProvider {
    * @returns Array of { id, matchCount } sorted by matchCount descending
    */
   async getIdsForTextQuery(query: string): Promise<Array<{ id: string; matchCount: number }>> {
+    return this.scoreTextQuery(query)
+  }
+
+  /**
+   * Score a text query over `ids` ONLY — the reference implementation of the
+   * optional `getIdsForTextQueryWithin` door (see
+   * {@link import('../plugin.js').MetadataIndexProvider}). The hybrid
+   * `find({ query, where })` path passes the metadata filter's universe here so
+   * the text leg ranks INSIDE that universe instead of ranking the whole store
+   * and discarding the rows the filter would have dropped.
+   *
+   * It answers from the same posting-list merge as {@link getIdsForTextQuery},
+   * with the candidate membership applied as each word's postings are counted,
+   * so the two doors can never disagree: the answer is exactly the whole-store
+   * answer restricted to `ids`, in the same order.
+   *
+   * @param query - Text query to search for.
+   * @param ids - Candidate entity ids; only these may appear in the answer.
+   * @returns Array of { id, matchCount } sorted by matchCount descending.
+   */
+  async getIdsForTextQueryWithin(
+    query: string,
+    ids: readonly string[]
+  ): Promise<Array<{ id: string; matchCount: number }>> {
+    if (ids.length === 0) return []
+    return this.scoreTextQuery(query, new Set(ids))
+  }
+
+  /**
+   * The one posting-list merge behind both text doors.
+   *
+   * Each query word contributes AT MOST one match per entity (a posting list
+   * can name an id more than once), and entities are ranked by how many of the
+   * query's words they matched. `within`, when given, restricts the count to
+   * those candidates — applied during the merge, so a restricted call never
+   * materializes a whole-store match map.
+   *
+   * @param query - Text query to search for.
+   * @param within - Optional candidate universe; absent = the whole store.
+   * @returns Array of { id, matchCount } sorted by matchCount descending.
+   */
+  private async scoreTextQuery(
+    query: string,
+    within?: ReadonlySet<string>
+  ): Promise<Array<{ id: string; matchCount: number }>> {
     const queryWords = this.tokenize(query)
     if (queryWords.length === 0) return []
 
-    // Get IDs for each word hash
-    const wordIdSets: Map<string, number>[] = []
+    // Count matches per entity, one word's postings at a time.
+    const matchCounts = new Map<string, number>()
     for (const word of queryWords) {
       const wordHash = this.hashWord(word)
       let ids: string[]
@@ -1529,19 +1574,12 @@ export class MetadataIndexManager implements MetadataIndexProvider {
           throw err
         }
       }
-      const idSet = new Map<string, number>()
+      // One count per (word, entity) — dedupe this word's postings first.
+      const counted = new Set<string>()
       for (const id of ids) {
-        idSet.set(id, 1)
-      }
-      wordIdSets.push(idSet)
-    }
-
-    if (wordIdSets.length === 0) return []
-
-    // Count matches per entity
-    const matchCounts = new Map<string, number>()
-    for (const idSet of wordIdSets) {
-      for (const [id] of idSet) {
+        if (counted.has(id)) continue
+        counted.add(id)
+        if (within && !within.has(id)) continue
         matchCounts.set(id, (matchCounts.get(id) || 0) + 1)
       }
     }
@@ -2575,6 +2613,19 @@ export class MetadataIndexManager implements MetadataIndexProvider {
   /** Once-per-field flag for the fallback-degradation announcement. */
   private static announcedFallbackSorts = new Set<string>()
 
+  /**
+   * Evaluate `filter` over `ids` only — the graph-first find's door (the
+   * neighbour set filtered by id, never the store filtered and then
+   * intersected). This index answers from its own `getIdsForFilter`, so the
+   * two doors cannot disagree; the cost is that of the filter over this
+   * in-memory index, and the answer keeps the caller's order.
+   */
+  async filterIdsWithin(filter: any, ids: readonly string[]): Promise<string[]> {
+    if (ids.length === 0) return []
+    const matched = new Set(await this.getIdsForFilter(filter))
+    return ids.filter((id) => matched.has(id))
+  }
+
   async getSortedIdsForFilter(
     filter: any,
     orderBy: string,

src/vfs/VirtualFileSystem.ts

@@ -1572,7 +1572,19 @@ export class VirtualFileSystem implements IVirtualFileSystem {
   // ============= Semantic Operations =============
 
   /**
-   * Search files with natural language
+   * Search files with natural language.
+   *
+   * `options.path` scopes the search to a directory: its whole subtree by
+   * default, its immediate children when `recursive` is `false`. Both scopes
+   * are metadata filters the index SERVES, so the scope narrows the search
+   * before it runs — no tree walk, and never an over-fetch filtered afterwards.
+   *
+   * @param query - The natural-language query.
+   * @param options - Scope, metadata filters and paging (see {@link SearchOptions}).
+   * @returns The matching files, best first.
+   * @throws {VFSError} ENOENT when `recursive: false` names a path that does
+   *   not exist (the non-recursive scope is the directory's own identity, so
+   *   the directory has to be there).
    */
   async search(query: string, options?: SearchOptions): Promise<SearchResult[]> {
     await this.ensureInitialized()
@@ -1588,11 +1600,26 @@ export class VirtualFileSystem implements IVirtualFileSystem {
       }
     }
 
-    // Add path filter if specified
+    // Scope to a directory, if asked. This used to emit
+    // `path: { $startsWith }` — an operator that is not in the filter
+    // vocabulary at all, and whose `$`-less spelling the metadata index
+    // REFUSES by the served-operator law (an equality/range posting index
+    // cannot evaluate a substring without reading every row). Every
+    // path-scoped VFS search therefore threw, and none has ever worked on
+    // this engine line. Both scopes below are served shapes.
     if (options?.path) {
-      params.where = {
-        ...params.where,
-        path: { $startsWith: options.path }
+      if (options.recursive === false) {
+        // Immediate children only: the directory's identity IS the scope, and
+        // `parent` is an indexed equality on every VFS entity.
+        params.where = {
+          ...params.where,
+          parent: await this.pathResolver.resolve(options.path)
+        }
+      } else {
+        const scope = this.descendantPathScope(options.path)
+        if (scope) {
+          params.where = { ...params.where, path: scope }
+        }
       }
     }
 
@@ -1754,6 +1781,42 @@ export class VirtualFileSystem implements IVirtualFileSystem {
     return entity as VFSEntity
   }
 
+  /**
+   * The SERVED metadata shape for "everything under this directory".
+   *
+   * `metadata.path` is the VFS's truth — write and rename maintain it, and the
+   * `Contains` edges are a projection of it (see {@link repairContainment}) —
+   * it is indexed on every VFS entity, and the metadata index serves ordered
+   * range operators. So a subtree scope is a half-open range over the path
+   * column: O(log n + matches), no tree walk, and nothing fetched that the
+   * scope then discards.
+   *
+   * The range is `[dir + '/', dir + <successor of '/'>)`. Every descendant path
+   * begins with `dir + '/'`, and '0' is the code point directly after '/', so a
+   * string lies in the range EXACTLY when it carries that prefix. The two
+   * bounds differ at a single ASCII position, so the answer is the same under
+   * code-unit and code-point collation alike — no dependence on how the store
+   * orders the rest of the string.
+   *
+   * Sibling exclusion falls out of the same fact and is worth stating, because
+   * it is where a naive prefix test goes wrong: for `dir = '/scope'`,
+   * `/scope-sibling/x` sorts BELOW the lower bound ('-' precedes '/') and
+   * `/scope0` sits at the open upper bound — both outside, while
+   * `/scope/sub/deep/c.txt` is inside at any depth.
+   *
+   * @param path - The directory to scope to.
+   * @returns The `where` fragment for the `path` field, or `null` for the root
+   *   — every VFS entity is under it, so no clause narrows the search.
+   */
+  private descendantPathScope(path: string): { gte: string; lt: string } | null {
+    const dir = path.replace(/\/+/g, '/').replace(/\/$/, '') || '/'
+    if (dir === '/') return null
+    // Computed, so the bound carries its own reason: the first string that can
+    // no longer share the `dir + '/'` prefix.
+    const separatorSuccessor = String.fromCharCode('/'.charCodeAt(0) + 1)
+    return { gte: `${dir}/`, lt: `${dir}${separatorSuccessor}` }
+  }
+
   private getParentPath(path: string): string {
     const normalized = path.replace(/\/+/g, '/').replace(/\/$/, '')
     const lastSlash = normalized.lastIndexOf('/')
@@ -2295,6 +2358,31 @@ export class VirtualFileSystem implements IVirtualFileSystem {
       cursor = page.nextCursor
     }
 
+    // Pass 2: ONE paged walk over every Contains edge, grouped by target in
+    // memory. The earlier shape issued one awaited related({ to }) per VFS
+    // entity — O(entities) serialized graph calls, measured in whole minutes
+    // on large brains. This shape is O(edges / page) calls regardless of how
+    // many entities exist; mutations alone stay per-defect.
+    const incomingByTarget = new Map<string, Relation<any>[]>()
+    {
+      const pageSize = 1000
+      let pageOffset = 0
+      for (;;) {
+        const page = await this.brain.related({
+          type: VerbType.Contains,
+          limit: pageSize,
+          offset: pageOffset
+        })
+        for (const edge of page) {
+          const bucket = incomingByTarget.get(edge.to)
+          if (bucket) bucket.push(edge)
+          else incomingByTarget.set(edge.to, [edge])
+        }
+        if (page.length < pageSize) break
+        pageOffset += pageSize
+      }
+    }
+
     let removed = 0
     let restored = 0
     for (const { id, path } of vfsEntities) {
@@ -2307,7 +2395,7 @@ export class VirtualFileSystem implements IVirtualFileSystem {
         continue
       }
 
-      const incoming = await this.brain.related({ to: id, type: VerbType.Contains })
+      const incoming = incomingByTarget.get(id) ?? []
       let expectedSeen = false
       for (const edge of incoming) {
         const isVfsEdge = edge.subtype === 'vfs-contains' || (edge.metadata as any)?.isVFS === true

tests/configs/vitest.perf.config.ts

@@ -0,0 +1,68 @@
+import { defineConfig } from 'vitest/config'
+
+/**
+ * Perf/scale + environment-dependent test configuration.
+ *
+ * The exclusive on-demand slot for everything the correctness gate
+ * (`vitest.config.ts`, the config a bare `vitest run` picks up) excludes:
+ * wall-clock/scale benchmarks and the two tests whose outcome depends on
+ * the host machine or network rather than the code. See CONTRIBUTING.md's
+ * "Test gate" section and the exclude list in `vitest.config.ts` (root) for
+ * why each file lives here instead of the gate.
+ *
+ * `include` names this set explicitly — it is the mirror image of the
+ * root config's exclude list, not an independent glob, so the two stay in
+ * sync by inspection. Longer timeouts than the gate's 120s/60s: one case in
+ * tests/critical-performance-benchmark.test.ts measures ~128s of real work.
+ */
+export default defineConfig({
+  test: {
+    globals: true,
+    setupFiles: ['./tests/setup.ts'],
+    environment: 'node',
+
+    // The marker a test uses to tell it is running under this lane (see
+    // tests/integration/storage-batch-operations.test.ts's batch-vs-
+    // individual timing case) — a wall-clock RATIO assertion self-skips
+    // with a reason when this is absent, rather than flaking the
+    // correctness gate on whichever path happens to be faster this build.
+    env: { BRAINY_PERF_LANE: '1' },
+
+    // Sequential, single fork — same isolation the gate uses, so a perf
+    // measurement isn't skewed by sibling test contention.
+    pool: 'forks',
+    poolOptions: {
+      forks: {
+        maxForks: 1,
+        minForks: 1,
+        singleFork: true,
+        isolate: true
+      }
+    },
+
+    testTimeout: 300000, // 5 minutes per test (the 128s case plus headroom)
+    hookTimeout: 120000,
+    teardownTimeout: 10000,
+
+    maxConcurrency: 1,
+    fileParallelism: false,
+
+    include: [
+      'tests/performance/**/*.{test,spec}.{js,ts}',
+      'tests/critical-performance-benchmark.test.ts',
+      'tests/api/performance-benchmarks.test.ts',
+      'tests/package-size-limit.test.ts',
+      'tests/model-loading.test.ts',
+      // Not a whole perf file — one wall-clock-ratio case inside an
+      // otherwise-correctness integration suite (self-skipped everywhere
+      // else via BRAINY_PERF_LANE). Stays in the integration gate's
+      // include too, so every OTHER test in the file keeps running there.
+      'tests/integration/storage-batch-operations.test.ts'
+    ],
+
+    reporters: process.env.CI ? ['dot'] : ['basic'],
+
+    retry: process.env.CI ? 1 : 0,
+    shard: process.env.VITEST_SHARD
+  }
+})

tests/integration/counts-persist-single-flight.test.ts

@@ -0,0 +1,111 @@
+/**
+ * @module tests/integration/counts-persist-single-flight
+ * @description Regression for a production race in FileSystemStorage's
+ * counts ledger: `persistCounts()` was write-through on every count change
+ * with no serialization, and the atomic writer named its temp file with
+ * millisecond granularity (`.tmp-<pid>-<ms>`). Two persists inside one
+ * millisecond shared the temp path — both wrote it, the first rename
+ * consumed it, the second rename found nothing: ENOENT, ~1,500 times a day
+ * on a busy production brain, with a full ledger write per change behind it.
+ *
+ * Under pin: persists are single-flight and coalesced — one in flight, at
+ * most one trailing pass carrying the burst's final state — and every atomic
+ * write owns a unique temp path. A burst of N count changes costs at most
+ * two ledger writes, never errors, and leaves a ledger equal to memory.
+ */
+import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest'
+import * as fs from 'node:fs'
+import * as os from 'node:os'
+import * as path from 'node:path'
+import { Brainy } from '../../src/brainy.js'
+import { NounType } from '../../src/types/graphTypes.js'
+
+describe('counts persistence is single-flight, coalesced, and never races its own temp file', () => {
+  let dir: string
+  let brain: any
+
+  beforeEach(async () => {
+    process.env.BRAINY_DETERMINISTIC_EMBEDDINGS = 'true'
+    dir = fs.mkdtempSync(path.join(os.tmpdir(), 'brainy-counts-race-'))
+    brain = new Brainy({
+      requireSubtype: false,
+      storage: { type: 'filesystem', path: dir },
+      dimensions: 384,
+      silent: true
+    })
+    await brain.init()
+  })
+
+  afterEach(async () => {
+    vi.restoreAllMocks()
+    await brain.close()
+    fs.rmSync(dir, { recursive: true, force: true })
+  })
+
+  it('a burst of concurrent count changes → at most two ledger writes, zero errors, ledger == memory', async () => {
+    const storage = brain.storage
+    const countsPath: string = storage.countsFilePath
+    expect(countsPath, 'the filesystem adapter persists a counts ledger').toBeTruthy()
+
+    // Let init's own persists settle so the burst is measured alone.
+    await storage.flushCounts?.()
+
+    const renameSpy = vi.spyOn(fs.promises, 'rename')
+    const errorSpy = vi.spyOn(console, 'error')
+
+    // Twenty-five concurrent count changes — the shape of a write burst; each
+    // used to launch its own persist.
+    const BURST = 25
+    await Promise.all(
+      Array.from({ length: BURST }, () => storage.scheduleCountPersist())
+    )
+
+    const ledgerRenames = renameSpy.mock.calls.filter(([, to]) => String(to) === countsPath)
+    expect(ledgerRenames.length, 'single-flight + one trailing pass').toBeLessThanOrEqual(2)
+    expect(ledgerRenames.length, 'the burst was persisted at all').toBeGreaterThanOrEqual(1)
+
+    const persistErrors = errorSpy.mock.calls.filter((args) => String(args[0]).includes('persisting counts'))
+    expect(persistErrors).toEqual([])
+
+    const ledger = JSON.parse(fs.readFileSync(countsPath, 'utf-8'))
+    expect(ledger.totalNounCount).toBe(storage.totalNounCount)
+    expect(ledger.totalVerbCount).toBe(storage.totalVerbCount)
+  })
+
+  it('real writes in parallel: the ledger lands complete and no persist error is logged', async () => {
+    const storage = brain.storage
+    const countsPath: string = storage.countsFilePath
+    const errorSpy = vi.spyOn(console, 'error')
+
+    await Promise.all(
+      Array.from({ length: 12 }, (_, i) =>
+        brain.add({ data: `burst row ${i}`, type: NounType.Thing })
+      )
+    )
+    await storage.flushCounts?.()
+
+    const persistErrors = errorSpy.mock.calls.filter((args) => String(args[0]).includes('persisting counts'))
+    expect(persistErrors).toEqual([])
+    const ledger = JSON.parse(fs.readFileSync(countsPath, 'utf-8'))
+    expect(ledger.totalNounCount).toBe(storage.totalNounCount)
+    expect(await brain.getNounCount()).toBe(ledger.totalNounCount)
+  })
+
+  it('every atomic write owns its own temp path — two writes in one millisecond never collide', async () => {
+    const storage = brain.storage
+    const tmpNames: string[] = []
+    vi.spyOn(fs.promises, 'writeFile').mockImplementation(async (p: any) => {
+      tmpNames.push(String(p))
+    })
+    vi.spyOn(fs.promises, 'rename').mockImplementation(async () => undefined)
+    const target = path.join(dir, 'probe.json')
+    await Promise.all([
+      storage.writeFileAtomic(target, '{"a":1}'),
+      storage.writeFileAtomic(target, '{"a":2}'),
+      storage.writeFileAtomic(target, '{"a":3}')
+    ])
+    const probeTmps = tmpNames.filter((n) => n.startsWith(`${target}.tmp-`))
+    expect(probeTmps.length).toBe(3)
+    expect(new Set(probeTmps).size, 'no two writes shared a temp path').toBe(3)
+  })
+})

tests/integration/entity-tree-stamp.test.ts

@@ -57,7 +57,11 @@ describe('entity-tree family stamp', () => {
     const invariants = (stamp.members as any).invariants
     expect(invariants.nounCount).toBe(await brain.storage.getNounCount())
     expect(invariants.verbCount).toBe(await brain.storage.getVerbCount())
-    expect(stamp.sourceGeneration).toBe(brain.generation())
+    // THE SOURCE IS COMMITTED TRUTH, never the allocated counter. Stamping the
+    // counter labelled the stamp with a generation a write in flight had merely
+    // claimed, so every crash inside a write window produced a spurious verdict
+    // at the next open (see the torn-tail pins below).
+    expect(stamp.sourceGeneration).toBe(brain.generationStore.committedGeneration())
     expect(stamp.generation).toBeGreaterThanOrEqual(1)
   })
 
@@ -112,6 +116,96 @@ describe('entity-tree family stamp', () => {
     expect(stillIncoherent).toEqual([])
   })
 
+  /**
+   * Rewrite the on-disk stamp so its `sourceGeneration` sits ABOVE the store's
+   * committed watermark — the durable shape a torn generation-log tail leaves
+   * behind (the stamp's fsync outlived the tail's). Fabricated rather than
+   * crash-produced so the pin is deterministic; the seeded-SIGKILL lane
+   * (`scripts/crash-consistency.mjs` in the engine repo) produces the same
+   * shape from a real abrupt termination.
+   */
+  const fabricateTear = (ahead: number): FamilyStamp => {
+    const file = path.join(dir, `${ENTITY_TREE_STAMP_PATH}.gz`)
+    const zlib = require('node:zlib')
+    const raw = JSON.parse(zlib.gunzipSync(fs.readFileSync(file)).toString('utf-8')) as FamilyStamp
+    const torn: FamilyStamp = { ...raw, sourceGeneration: raw.sourceGeneration + ahead }
+    fs.writeFileSync(file, zlib.gzipSync(JSON.stringify(torn)))
+    return torn
+  }
+
+  it('a torn generation-log tail is a TERMINAL VERDICT at open: narrated, demoted, never a wait', async () => {
+    for (let i = 0; i < 3; i++)
+      await brain.add({ data: `torn${i}`, type: 'document', metadata: { i } })
+    await brain.close()
+    const torn = fabricateTear(5)
+
+    const warn = vi.spyOn(prodLog, 'warn')
+    const startedAt = Date.now()
+    brain = await open()
+    const openMs = Date.now() - startedAt
+
+    const tearLines = warn.mock.calls.filter((c) => String(c[0]).includes('TORN GENERATION-LOG TAIL'))
+    expect(tearLines.length).toBe(1)
+    const said = String(tearLines[0][0])
+    // Narrated PRECISELY: both generations, the file, and the named cure.
+    expect(said).toContain(`source generation ${torn.sourceGeneration}`)
+    expect(said).toContain(`committed generation ${brain.generationStore.committedGeneration()}`)
+    expect(said).toContain(ENTITY_TREE_STAMP_PATH)
+    expect(said).toContain('DEMOTED')
+    expect(said).toMatch(/repairIndex\(\)/)
+    // Terminal, not a wait: the demotion is O(1) straight-line work, so a tear
+    // cannot turn an open into the 8-minute spin this class was reported as.
+    expect(openMs).toBeLessThan(30_000)
+
+    // The store SERVES — a tear in a stamp never locks an owner out of the
+    // canonical tree the stamp merely describes.
+    expect((await brain.find({ type: 'document', limit: 100 })).length).toBe(3)
+
+    // The demotion CONVERGED: the stamp now names committed truth, and the
+    // next open is quiet. A verdict that re-narrates every open is a wait
+    // wearing a different hat.
+    const restamped = (await readFamilyStamp(brain.storage, ENTITY_TREE_STAMP_PATH)) as FamilyStamp
+    expect(restamped.sourceGeneration).toBe(brain.generationStore.committedGeneration())
+    await brain.close()
+    const warn2 = vi.spyOn(prodLog, 'warn')
+    brain = await open()
+    expect(warn2.mock.calls.filter((c) => String(c[0]).includes('TORN'))).toEqual([])
+  })
+
+  it('a READ-ONLY open on a torn tail refuses to guess: terminal verdict + named cure, no re-stamp', async () => {
+    await brain.add({ data: 'ro', type: 'document', metadata: {} })
+    await brain.close()
+    const torn = fabricateTear(3)
+
+    const warn = vi.spyOn(prodLog, 'warn')
+    const reader: any = await Brainy.openReadOnly({
+      requireSubtype: false,
+      storage: { type: 'filesystem', path: dir },
+      silent: true,
+      dimensions: 384
+    })
+    const tearLines = warn.mock.calls.filter((c) => String(c[0]).includes('TORN GENERATION-LOG TAIL'))
+    expect(tearLines.length).toBe(1)
+    const said = String(tearLines[0][0])
+    expect(said).toContain('READ-ONLY')
+    expect(said).toContain('UNVERIFIED')
+    expect(said).toMatch(/repairIndex\(\)/)
+    await reader.close()
+
+    // A reader never rewrites the store: read the bytes back off disk (not
+    // through a writer open, which would demote them) — the torn stamp is
+    // exactly as it was found.
+    const onDisk = JSON.parse(
+      require('node:zlib')
+        .gunzipSync(fs.readFileSync(path.join(dir, `${ENTITY_TREE_STAMP_PATH}.gz`)))
+        .toString('utf-8')
+    ) as FamilyStamp
+    expect(onDisk.sourceGeneration).toBe(torn.sourceGeneration)
+    expect(onDisk.generation).toBe(torn.generation)
+
+    brain = await open()
+  })
+
   it('the one verifier handles both member modes', () => {
     const rollup: FamilyStamp = {
       family: 'x',
@@ -127,7 +221,13 @@ describe('entity-tree family stamp', () => {
       stampSource: 5,
       head: 9
     })
-    expect(verifyFamilyStamp(rollup, 3, { nounCount: 10 }).state).toBe('incoherent') // ahead of head
+    // AHEAD is its own class — a torn generation-log tail, never folded in
+    // with `incoherent`: the two have opposite cures (recount vs demote).
+    expect(verifyFamilyStamp(rollup, 3, { nounCount: 10 })).toEqual({
+      state: 'torn',
+      stampSource: 5,
+      head: 3
+    })
     expect(verifyFamilyStamp(null, 5, {})).toEqual({ state: 'absent' })
 
     const enumerated: FamilyStamp = {

tests/integration/factlog-open-prune.test.ts

@@ -0,0 +1,360 @@
+/**
+ * @module tests/integration/factlog-open-prune
+ * @description THE OPEN READS THE TAIL, NOT THE HISTORY.
+ *
+ * Every log-authority open asks the fact log one question — "is there a fact
+ * above the committed pointer?" — and until this lane existed it answered by
+ * reading and CRC-decoding EVERY segment file the manifest names. MEASURED in
+ * production on a 16k-row brain at generation ~478,819: 34-37 seconds inside
+ * the `generation-store-open-fold` phase, on every open, including the clean
+ * one where the answer is always "nothing".
+ *
+ * The manifest already records each sealed segment's `lastGeneration`, written
+ * at seal time AFTER the segment's bytes are fsynced and into a manifest that
+ * is itself written atomically and fsynced — and a sealed file is never
+ * appended to again (the same manifest flip re-points `tailSegment`). So an
+ * entry recording `lastGeneration ≤ committed` PROVES its file holds nothing
+ * above the bound, and the open can skip it whole.
+ *
+ * Pinned here, from the log's own counters (the narration line), never a clock:
+ *
+ *   1. A clean close and reopen on a log with ≥4 sealed segments reads
+ *      EXACTLY the tail (1 of 6), prunes the rest, and finds nothing.
+ *   2. A real SIGKILLed process that sealed segments holding facts ABOVE the
+ *      committed pointer: the reopen READS those sealed segments and recovers
+ *      byte-identically to an unpruned open (differential — the same store,
+ *      with the provable field stripped from its manifest, takes the full-scan
+ *      path and must agree fact for fact, before and after `open()`).
+ *   3. A manifest entry with no `lastGeneration` (legacy, or hand-repaired) is
+ *      READ. Never prune what the manifest cannot prove.
+ */
+import { describe, it, expect, afterEach } from 'vitest'
+import * as fs from 'node:fs'
+import * as os from 'node:os'
+import * as path from 'node:path'
+import { spawn } from 'node:child_process'
+import {
+  FactLog,
+  FACTS_MANIFEST_PATH,
+  type CommitFact,
+  type FactLogStorage
+} from '../../src/db/factLog.js'
+import { FileSystemStorage } from '../../src/storage/adapters/fileSystemStorage.js'
+
+const REPO_ROOT = process.cwd()
+const TSX = path.join(REPO_ROOT, 'node_modules', '.bin', 'tsx')
+/** ~1KB frames against a 4KB rotation threshold: ~5 facts per segment. */
+const ROTATE_BYTES = 4096
+
+const tmpDirs: string[] = []
+function makeTempDir(): string {
+  const dir = fs.mkdtempSync(path.join(os.tmpdir(), 'brainy-factlog-prune-'))
+  tmpDirs.push(dir)
+  return dir
+}
+
+afterEach(() => {
+  for (const dir of tmpDirs.splice(0)) {
+    try {
+      fs.rmSync(dir, { recursive: true, force: true })
+    } catch {
+      /* best effort */
+    }
+    try {
+      fs.rmSync(`${dir}.ready.json`, { force: true })
+    } catch {
+      /* best effort */
+    }
+  }
+})
+
+const UUID = (n: number): string => `00000000-0000-4000-8000-${String(n).padStart(12, '0')}`
+
+/** One ~1KB fact — the padding is what makes rotation cheap to provoke. */
+function fact(generation: number): CommitFact {
+  return {
+    generation,
+    timestamp: 1_700_000_000_000 + generation,
+    ops: [
+      {
+        kind: 'noun',
+        id: UUID(generation),
+        record: {
+          metadata: { noun: 'document', pad: 'x'.repeat(900), g: generation },
+          vector: null
+        }
+      }
+    ]
+  }
+}
+
+/**
+ * A deterministic int minter so the log writes the V2 format production
+ * writes (the prune is a manifest-level decision and never touches segment
+ * bytes — but the pins should run against the bytes the fleet actually has).
+ */
+function makeMinter(): (kind: 'noun' | 'verb', id: string) => bigint {
+  const ints = new Map<string, bigint>()
+  return (kind, id) => {
+    const key = `${kind}:${id}`
+    let minted = ints.get(key)
+    if (minted === undefined) {
+      minted = BigInt(ints.size + 1)
+      ints.set(key, minted)
+    }
+    return minted
+  }
+}
+
+/** Open a fact log over a store directory (a fresh adapter each time — this is
+ *  what a reopen actually does). */
+async function openStore(dir: string): Promise<{ storage: any; log: FactLog }> {
+  const storage: any = new FileSystemStorage(dir)
+  await storage.init()
+  const log = new FactLog(storage as FactLogStorage, { rotateBytes: ROTATE_BYTES })
+  log.setIntMinter(makeMinter())
+  return { storage, log }
+}
+
+/** Build a log of `count` facts (rotating every ~5), left durable, not closed. */
+async function buildLog(dir: string, count: number): Promise<number> {
+  const { log } = await openStore(dir)
+  await log.open(0)
+  for (let g = 1; g <= count; g++) await log.append(fact(g))
+  await log.sync()
+  return log.headGeneration()
+}
+
+/** Capture the narration channel (`prodLog.narrate` → console.warn). */
+async function captureNarration<T>(
+  fn: () => Promise<T>
+): Promise<{ result: T; lines: string[] }> {
+  const lines: string[] = []
+  const original = console.warn
+  console.warn = ((...args: unknown[]) => {
+    lines.push(args.map((a) => String(a)).join(' '))
+  }) as typeof console.warn
+  try {
+    return { result: await fn(), lines }
+  } finally {
+    console.warn = original
+  }
+}
+
+/** The counters the open narrated — the pin's only source of truth for what
+ *  was read (a wall-clock assertion could pass on a warm page cache). */
+function scanCounts(lines: string[]): { read: number; pruned: number; total: number } {
+  const line = lines.find((l) => l.includes('[FactLog] above-manifest peek above generation'))
+  if (!line) {
+    throw new Error(`no peek narration in:\n${lines.join('\n')}`)
+  }
+  const match = /(\d+) segment\(s\) read, (\d+) pruned of (\d+)/.exec(line)
+  if (!match) throw new Error(`unparsable peek narration: ${line}`)
+  return { read: Number(match[1]), pruned: Number(match[2]), total: Number(match[3]) }
+}
+
+interface SegmentEntryOnDisk {
+  file: string
+  firstGeneration: number
+  lastGeneration?: number
+  facts: number
+  bytes: number
+}
+
+async function readManifest(dir: string): Promise<{
+  segments: SegmentEntryOnDisk[]
+  tailSegment: string | null
+}> {
+  const storage: any = new FileSystemStorage(dir)
+  await storage.init()
+  return (await storage.readRawObject(FACTS_MANIFEST_PATH)) as any
+}
+
+async function rewriteManifest(
+  dir: string,
+  mutate: (manifest: any) => void
+): Promise<void> {
+  const storage: any = new FileSystemStorage(dir)
+  await storage.init()
+  const manifest = await storage.readRawObject(FACTS_MANIFEST_PATH)
+  mutate(manifest)
+  await storage.writeRawObject(FACTS_MANIFEST_PATH, manifest)
+  await storage.syncRawObjects([FACTS_MANIFEST_PATH])
+}
+
+/** Every fact the log holds, in order — the recovered state, read back. */
+async function allFacts(log: FactLog): Promise<CommitFact[]> {
+  const out: CommitFact[] = []
+  const handle = log.scanFacts()
+  for await (const batch of handle.batches()) out.push(...batch.facts)
+  return out
+}
+
+describe('fact log — the open reads only the segments that can hold facts above the bound', () => {
+  it('a clean close + reopen over ≥4 sealed segments reads exactly the tail and finds nothing', async () => {
+    const dir = makeTempDir()
+    const head = await buildLog(dir, 30)
+
+    const manifest = await readManifest(dir)
+    expect(manifest.segments.length).toBeGreaterThanOrEqual(4) // the fixture is real
+    expect(manifest.tailSegment).not.toBeNull()
+
+    // The reopen: a clean close means committed === the log's head.
+    const { log } = await openStore(dir)
+    const { result: orphans, lines } = await captureNarration(() => log.peekFactsAbove(head))
+
+    expect(orphans).toEqual([]) // the fold finds nothing, as it always does after a clean close
+    const counts = scanCounts(lines)
+    expect(counts.read).toBe(1) // EXACTLY the tail
+    expect(counts.total).toBe(manifest.segments.length + 1)
+    expect(counts.pruned).toBe(manifest.segments.length)
+
+    // And the reconciling open still lands on the same committed prefix.
+    await log.open(head)
+    expect(log.headGeneration()).toBe(head)
+    expect((await allFacts(log)).map((f) => f.generation)).toEqual(
+      Array.from({ length: head }, (_, i) => i + 1)
+    )
+  })
+
+  it('a manifest entry with no lastGeneration is READ — never prune what you cannot prove', async () => {
+    const dir = makeTempDir()
+    const head = await buildLog(dir, 30)
+    const before = await readManifest(dir)
+    expect(before.segments.length).toBeGreaterThanOrEqual(4)
+
+    // A legacy/hand-repaired entry: the field the prune needs is simply absent.
+    await rewriteManifest(dir, (m) => {
+      delete m.segments[0].lastGeneration
+    })
+
+    const { log } = await openStore(dir)
+    const { result: orphans, lines } = await captureNarration(() => log.peekFactsAbove(head))
+
+    expect(orphans).toEqual([]) // still nothing above the bound — it was READ to find out
+    const counts = scanCounts(lines)
+    expect(counts.read).toBe(2) // the unprovable entry + the tail
+    expect(counts.pruned).toBe(before.segments.length - 1)
+    expect(counts.total).toBe(before.segments.length + 1)
+  })
+
+  it(
+    'a SIGKILLed writer that sealed segments above the committed pointer recovers identically to an unpruned open',
+    async () => {
+      const dir = makeTempDir()
+      const readyPath = `${dir}.ready.json`
+      // A real process death: the child fsyncs its segments, records what it
+      // reached, and SIGKILLs ITSELF — no close, no unwind, no chance to tidy.
+      const script = `
+        import * as fs from 'node:fs'
+        import { FactLog } from ${JSON.stringify(path.join(REPO_ROOT, 'src', 'db', 'factLog.ts'))}
+        import { FileSystemStorage } from ${JSON.stringify(path.join(REPO_ROOT, 'src', 'storage', 'adapters', 'fileSystemStorage.ts'))}
+        const UUID = (n) => '00000000-0000-4000-8000-' + String(n).padStart(12, '0')
+        const fact = (g) => ({
+          generation: g,
+          timestamp: 1700000000000 + g,
+          ops: [{ kind: 'noun', id: UUID(g), record: { metadata: { noun: 'document', pad: 'x'.repeat(900), g }, vector: null } }]
+        })
+        const ints = new Map()
+        const storage = new FileSystemStorage(${JSON.stringify(dir)})
+        await storage.init()
+        const log = new FactLog(storage, { rotateBytes: ${ROTATE_BYTES} })
+        log.setIntMinter((kind, id) => {
+          const key = kind + ':' + id
+          if (!ints.has(key)) ints.set(key, BigInt(ints.size + 1))
+          return ints.get(key)
+        })
+        await log.open(0)
+        for (let g = 1; g <= 30; g++) await log.append(fact(g))
+        await log.sync()
+        fs.writeFileSync(${JSON.stringify(readyPath)}, JSON.stringify({ head: log.headGeneration() }))
+        process.kill(process.pid, 'SIGKILL')
+      `
+      const scriptPath = path.join(dir, 'crash-writer.mts')
+      fs.writeFileSync(scriptPath, script)
+      const child = spawn(TSX, [scriptPath], { cwd: REPO_ROOT, stdio: ['ignore', 'pipe', 'pipe'] })
+      let output = ''
+      child.stdout.on('data', (d) => { output += String(d) })
+      child.stderr.on('data', (d) => { output += String(d) })
+      const exit = await new Promise<{ code: number | null; signal: string | null }>((resolve) =>
+        child.on('exit', (code, signal) => resolve({ code, signal }))
+      )
+      if (!fs.existsSync(readyPath)) {
+        throw new Error(`the crash writer never reached its kill point:\n${output}`)
+      }
+      // Death, not a shutdown: no close(), no unwind, no orderly exit code.
+      expect(exit.signal ?? `code ${exit.code}`).not.toBe('code 0')
+      const head = JSON.parse(fs.readFileSync(readyPath, 'utf8')).head as number
+      expect(head).toBe(30)
+
+      // The committed pointer the survivor comes back on: mid-log, so sealed
+      // segments hold facts ABOVE it — the exact shape the prune must not skip.
+      const committed = 12
+      const manifest = await readManifest(dir)
+      const straddling = manifest.segments.filter(
+        (s) => s.firstGeneration <= committed && (s.lastGeneration ?? 0) > committed
+      )
+      const entirelyAbove = manifest.segments.filter((s) => s.firstGeneration > committed)
+      expect(straddling.length).toBeGreaterThanOrEqual(1)
+      expect(entirelyAbove.length).toBeGreaterThanOrEqual(1)
+
+      // THE DIFFERENTIAL. The unpruned answer, through the SAME code on the
+      // SAME bytes: a peek above generation 0 can prune nothing (no sealed
+      // segment ends at or below 0), so it reads every segment file and
+      // decodes every frame — exactly what this open used to do — and its
+      // facts above the pointer are what the fold is entitled to replay.
+      const { log } = await openStore(dir)
+      const { result: fullScan, lines: fullLines } = await captureNarration(() =>
+        log.peekFactsAbove(0)
+      )
+      expect(scanCounts(fullLines)).toEqual({
+        read: manifest.segments.length + 1,
+        pruned: 0,
+        total: manifest.segments.length + 1
+      })
+      const unprunedAnswer = fullScan.filter((f) => f.generation > committed)
+
+      const { result: prunedAnswer, lines } = await captureNarration(() =>
+        log.peekFactsAbove(committed)
+      )
+
+      // The sealed segments above the bound were READ, not skipped.
+      const counts = scanCounts(lines)
+      expect(counts.read).toBe(straddling.length + entirelyAbove.length + 1)
+      expect(counts.pruned).toBe(manifest.segments.length - straddling.length - entirelyAbove.length)
+      expect(counts.pruned).toBeGreaterThan(0) // the prune did engage, and was still right
+      expect(prunedAnswer.map((f) => f.generation)).toEqual(
+        Array.from({ length: head - committed }, (_, i) => committed + 1 + i)
+      )
+      // Facts that live in a SEALED segment (not the tail) came back.
+      expect(prunedAnswer.some((f) => f.generation <= (straddling[0].lastGeneration ?? 0))).toBe(
+        true
+      )
+      // Fact for fact, the pruned answer IS the unpruned answer — so whatever
+      // the recovery replays, it replays identically.
+      expect(prunedAnswer).toEqual(unprunedAnswer)
+
+      // The fold's streaming twin (the unclean-open path) agrees too.
+      const streamed: CommitFact[] = []
+      for await (const batch of log.streamFactsAbove(committed)) streamed.push(...batch)
+      expect(streamed).toEqual(unprunedAnswer)
+
+      // And the reconciling open rolls back exactly as it always did: the two
+      // never-committed sealed segments dropped, the straddling one cut, the
+      // tail truncated — the log left as the committed prefix.
+      await log.open(committed)
+      expect(log.headGeneration()).toBe(committed)
+      expect((await allFacts(log)).map((f) => f.generation)).toEqual(
+        Array.from({ length: committed }, (_, i) => i + 1)
+      )
+      const after = await readManifest(dir)
+      expect(after.segments.map((s) => s.file)).toEqual(
+        manifest.segments
+          .filter((s) => s.firstGeneration <= committed)
+          .map((s) => s.file)
+      )
+      expect(after.segments[after.segments.length - 1].lastGeneration).toBe(committed)
+    },
+    120_000
+  )
+})

tests/integration/find-connected-order.test.ts

@@ -0,0 +1,165 @@
+/**
+ * @module tests/integration/find-connected-order
+ * @description The graph-first law for `find({ connected })` (10.4.8).
+ *
+ * With `connected` present the neighbour set is the candidate universe: it is
+ * resolved from the adjacency first, the metadata filter is evaluated over
+ * those ids only, and the page is cut last. The earlier order materialized the
+ * whole-store filtered id list, paged it, hydrated the page, and only then
+ * intersected with the neighbours — so a neighbour outside the first page of
+ * the filtered STORE was silently dropped, and every call paid O(store).
+ *
+ * These pins hold both halves. The answer: every matching neighbour is
+ * reachable by paging, a non-neighbour never appears, a negation (`missing`)
+ * is evaluated over the neighbours, `orderBy` sorts the whole neighbour set
+ * before the page is cut, and the vector leg walks the neighbours only. The
+ * cost shape: the metadata index is asked about the neighbour ids only, and
+ * hydration is one page — never the store.
+ */
+import { describe, it, expect, beforeAll, afterAll, vi } from 'vitest'
+import { Brainy } from '../../src/brainy'
+import { NounType, VerbType } from '../../src/types/graphTypes'
+import { v5 } from '../../src/universal/uuid'
+import { generateTestVector } from '../helpers/test-factory'
+
+/** Matching rows that are NOT neighbours — added FIRST, so the whole-store filtered list leads with them. */
+const NOISE = 120
+/** Matching rows that ARE neighbours of the anchor. */
+const NEIGHBOURS = 30
+/** Neighbours carrying `retracted: true` — excluded by the `missing` negation. */
+const RETRACTED = 4
+
+describe('find({ connected }) is graph-first: neighbours → filter → page', () => {
+  let brain: Brainy<any>
+  const anchor = 'anchor'
+  const sharedVector = generateTestVector()
+  const neighbourIds = new Set(Array.from({ length: NEIGHBOURS }, (_, i) => v5(`nb-${i}`)))
+
+  beforeAll(async () => {
+    brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+    await brain.add({
+      id: anchor,
+      data: 'the anchor',
+      type: NounType.Person,
+      metadata: { kind: 'anchor' },
+      vector: generateTestVector()
+    })
+    for (let i = 0; i < NOISE; i++) {
+      await brain.add({
+        id: `noise-${i}`,
+        data: `noise ${i}`,
+        type: NounType.Person,
+        metadata: { kind: 'note', rank: 1000 + i },
+        vector: sharedVector
+      })
+    }
+    for (let i = 0; i < NEIGHBOURS; i++) {
+      await brain.add({
+        id: `nb-${i}`,
+        data: `neighbour ${i}`,
+        type: NounType.Person,
+        metadata: { kind: 'note', rank: i + 1, ...(i < RETRACTED ? { retracted: true } : {}) },
+        vector: sharedVector
+      })
+      await brain.relate({ from: anchor, to: `nb-${i}`, type: VerbType.Knows })
+    }
+  })
+
+  afterAll(async () => {
+    brain = null as any
+  })
+
+  it('returns the matching neighbours page by page — none dropped, never a non-neighbour', async () => {
+    const seen = new Set<string>()
+    for (let offset = 0; offset <= NEIGHBOURS; offset += 10) {
+      const page = await brain.find({
+        connected: { from: anchor, direction: 'out' },
+        where: { kind: 'note' },
+        limit: 10,
+        offset
+      })
+      expect(page).toHaveLength(offset < NEIGHBOURS ? 10 : 0)
+      for (const r of page) {
+        expect(neighbourIds.has(r.entity.id)).toBe(true)
+        expect(seen.has(r.entity.id)).toBe(false)
+        seen.add(r.entity.id)
+      }
+    }
+    expect(seen.size).toBe(NEIGHBOURS)
+  })
+
+  it('evaluates a negation (`missing`) over the neighbour set, not the store', async () => {
+    const results = await brain.find({
+      connected: { from: anchor, direction: 'out' },
+      where: { kind: 'note', retracted: { missing: true } },
+      limit: 100
+    })
+    expect(results).toHaveLength(NEIGHBOURS - RETRACTED)
+    for (const r of results) {
+      expect(neighbourIds.has(r.entity.id)).toBe(true)
+      expect(r.entity.metadata.retracted).toBeUndefined()
+    }
+  })
+
+  it('asks the metadata index about the neighbour ids only, and hydrates one page', async () => {
+    const index = (brain as any).metadataIndex
+    const within = vi.spyOn(index, 'filterIdsWithin')
+    const hydrate = vi.spyOn(brain as any, 'batchGet')
+    try {
+      const results = await brain.find({
+        connected: { from: anchor, direction: 'out' },
+        where: { kind: 'note' },
+        limit: 10
+      })
+      expect(results).toHaveLength(10)
+      expect(within).toHaveBeenCalledTimes(1)
+      const askedIds = within.mock.calls[0][1] as string[]
+      expect(askedIds).toHaveLength(NEIGHBOURS)
+      for (const id of askedIds) expect(neighbourIds.has(id)).toBe(true)
+      expect(hydrate).toHaveBeenCalledTimes(1)
+      expect(hydrate.mock.calls[0][0]).toHaveLength(10)
+    } finally {
+      within.mockRestore()
+      hydrate.mockRestore()
+    }
+  })
+
+  it('orders the WHOLE neighbour set before cutting the page', async () => {
+    const results = await brain.find({
+      connected: { from: anchor, direction: 'out' },
+      where: { kind: 'note' },
+      orderBy: 'rank',
+      order: 'desc',
+      limit: 5
+    })
+    expect(results.map((r) => r.entity.metadata.rank)).toEqual([30, 29, 28, 27, 26])
+  })
+
+  it('walks the vector leg over the neighbours only', async () => {
+    const results = await brain.find({
+      vector: sharedVector,
+      connected: { from: anchor, direction: 'out' },
+      where: { kind: 'note' },
+      limit: 5
+    })
+    expect(results).toHaveLength(5)
+    for (const r of results) expect(neighbourIds.has(r.entity.id)).toBe(true)
+  })
+
+  it('an anchor without neighbours answers [] before the filter is asked', async () => {
+    const index = (brain as any).metadataIndex
+    const within = vi.spyOn(index, 'filterIdsWithin')
+    try {
+      const results = await brain.find({
+        connected: { from: 'noise-0', direction: 'out' },
+        where: { kind: 'note' },
+        limit: 10
+      })
+      expect(results).toEqual([])
+      expect(within).not.toHaveBeenCalled()
+    } finally {
+      within.mockRestore()
+    }
+  })
+})

tests/integration/find-hybrid-filter-before-hydrate.test.ts

@@ -0,0 +1,635 @@
+/**
+ * @module tests/integration/find-hybrid-filter-before-hydrate
+ * @description FILTER BEFORE HYDRATE, applied to the hybrid `find({ query })` path.
+ *
+ * A hybrid find fuses two legs. The semantic leg already walked only the
+ * metadata filter's universe (`candidateIds` / `allowedIds`). The TEXT leg did
+ * not: it ranked the WHOLE store, took the top `limit * 4`, read every one of
+ * those rows from canonical, and only then intersected with the filter — so a
+ * filtered hybrid find on a large store read hundreds of rows to return a
+ * handful of them, and a matching row outside the store-wide text prefix was
+ * silently dropped. That is the same defect `find({ connected })` carried
+ * before the graph-first law, one leg over.
+ *
+ * Both halves are pinned here.
+ *
+ * THE ANSWER. Where the filter did not truncate the text leg — the universe
+ * covers every text match, so both orders rank the same rows — the new
+ * pipeline's answer is IDENTICAL to the old one's: same rows, same order, same
+ * scores, same match visibility, same row shape. The oracle below is the
+ * pre-change pipeline itself, replayed on the same brain through the same
+ * doors, so the comparison is against what actually ran, not a remembered
+ * expectation.
+ *
+ * THE CORRECTION. Where the filter DID truncate it — the query's words are
+ * common outside the universe — the old order let the text leg contribute
+ * nothing at all: every row it ranked was discarded by the filter, and the
+ * answer came from the semantic leg alone. The new order ranks inside the
+ * universe, so the text leg contributes the rows it always should have.
+ *
+ * THE COST. Canonical is read for exactly the page: one batch, `limit` rows,
+ * never the legs. And the text leg is asked about the universe's ids only —
+ * what it marshals is bounded by the universe, not by the store.
+ */
+import { describe, it, expect, beforeAll, vi } from 'vitest'
+import { Brainy } from '../../src/brainy'
+import { NounType, VerbType } from '../../src/types/graphTypes'
+import { rankIndicesByScore, reorderByIndices } from '../../src/utils/resultRanking'
+import { resolveEntityId } from '../../src/utils/idNormalization'
+
+/** Embedding width of the default model — the row vectors must match it. */
+const DIM = 384
+
+/**
+ * A deterministic, per-row-distinct unit vector. Distinct so the semantic leg
+ * has a real ranking to produce (identical vectors would make its order a tie
+ * break), deterministic so the oracle and the pipeline see the same one.
+ */
+function seededVector(seed: number): number[] {
+  const v = new Array<number>(DIM)
+  for (let i = 0; i < DIM; i++) {
+    v[i] = Math.sin((i + 1) * 0.11 + seed * 0.37) * 0.5 + Math.cos((i + 1) * 0.05 + seed * 0.13) * 0.3
+  }
+  const magnitude = Math.sqrt(v.reduce((sum, x) => sum + x * x, 0))
+  return v.map((x) => x / magnitude)
+}
+
+/** The fields a caller reads off a hybrid row — the whole comparable surface. */
+function project(rows: any[]): any[] {
+  return rows.map((r) => ({
+    id: r.id,
+    score: r.score,
+    type: r.type,
+    metadata: r.metadata,
+    textMatches: r.textMatches,
+    textScore: r.textScore,
+    semanticScore: r.semanticScore,
+    matchSource: r.matchSource
+  }))
+}
+
+/**
+ * The PRE-CHANGE hybrid pipeline, replayed on a live brain through the same
+ * provider doors it used: whole-store text ranking with both legs hydrated in
+ * full, RRF fusion, then the metadata intersection, then the page.
+ *
+ * Supports the shapes these pins exercise (query + where/type/excludeVFS +
+ * connected + offset); `orderBy`, `fusion` and `near` are not replayed.
+ */
+async function legacyHybridFind(brain: any, params: any): Promise<any[]> {
+  const index = brain.metadataIndex
+  const limit = params.limit ?? 10
+  const offset = params.offset ?? 0
+  const hasFilter = Boolean(
+    params.where || params.type || params.subtype || params.service || params.excludeVFS
+  )
+
+  let preResolvedMetadataIds: string[] | null = null
+  let preResolvedFilter: any = null
+  let graphFirstIds: string[] | null = null
+
+  if (params.connected) {
+    // find() normalizes the anchors to canonical ids before this stage runs.
+    const anchored = {
+      ...params,
+      connected: {
+        ...params.connected,
+        ...(params.connected.from && { from: resolveEntityId(params.connected.from) }),
+        ...(params.connected.to && { to: resolveEntityId(params.connected.to) })
+      }
+    }
+    graphFirstIds = await brain.resolveConnectedIds(anchored)
+    if (graphFirstIds!.length > 0 && hasFilter) {
+      preResolvedFilter = brain.buildMetadataFilter(params)
+      graphFirstIds = await brain.filterIdsWithinBelted(preResolvedFilter, graphFirstIds)
+    }
+    if (graphFirstIds!.length === 0) return []
+    preResolvedMetadataIds = graphFirstIds
+  } else if (hasFilter) {
+    preResolvedFilter = brain.buildMetadataFilter(params)
+    preResolvedMetadataIds = await brain.filterIdsBelted(preResolvedFilter)
+    if (preResolvedMetadataIds!.length === 0) return []
+  }
+
+  // Text leg — the whole store, then the top `limit * 4`, hydrated in full.
+  const allTextMatches = await index.getIdsForTextQuery(params.query)
+  const topMatches = allTextMatches.slice(0, limit * 2 * 2)
+  const maxMatches = topMatches[0]?.matchCount || 1
+  const textEntities = await brain.batchGet(topMatches.map((m: any) => m.id))
+  const textResults = topMatches
+    .filter((m: any) => textEntities.has(m.id))
+    .map((m: any) => ({ id: m.id, score: m.matchCount / maxMatches }))
+
+  // Semantic leg — the beam walk over the universe, hydrated in full.
+  const vector = await brain.embed(params.query)
+  const searchOptions = preResolvedMetadataIds ? { candidateIds: preResolvedMetadataIds } : undefined
+  const searchResults: [string, number][] = await brain.index.search(
+    vector,
+    limit * 2,
+    undefined,
+    searchOptions
+  )
+  const semanticEntities = await brain.batchGet(searchResults.map(([id]) => id))
+  const semanticResults = searchResults
+    .filter(([id]) => semanticEntities.has(id))
+    .map(([id, distance]) => ({ id, score: Math.max(0, Math.min(1, 1 / (1 + distance))) }))
+
+  // RRF fusion, with the match visibility the rows carried.
+  const alpha = params.hybridAlpha ?? brain.autoAlpha(params.query)
+  const k = 60
+  const matchData = new Map<string, any>()
+  const textWeight = 1 - alpha
+  textResults.forEach((r: any, rank: number) => {
+    const existing = matchData.get(r.id) || { rrf: 0, hasText: false, hasSemantic: false }
+    existing.rrf += textWeight * (1 / (k + rank + 1))
+    existing.textScore = r.score
+    existing.hasText = true
+    matchData.set(r.id, existing)
+  })
+  semanticResults.forEach((r: any, rank: number) => {
+    const existing = matchData.get(r.id) || { rrf: 0, hasText: false, hasSemantic: false }
+    existing.rrf += alpha * (1 / (k + rank + 1))
+    existing.semanticScore = r.score
+    existing.hasSemantic = true
+    matchData.set(r.id, existing)
+  })
+
+  const queryWords: string[] = index.tokenize(params.query)
+  const textResultIds = new Set(textResults.map((r: any) => r.id))
+  const fusedIds = Array.from(matchData.entries())
+    .sort((a, b) => b[1].rrf - a[1].rrf)
+    .map(([id, data]) => ({ id, data }))
+
+  const allEntities = await brain.batchGet(fusedIds.map((f) => f.id))
+  let rows: any[] = []
+  for (const { id, data } of fusedIds) {
+    const entity = allEntities.get(id)
+    if (!entity) continue
+    const textContent = textResultIds.has(id)
+      ? index.extractTextContent({ data: entity.data, metadata: entity.metadata }).toLowerCase()
+      : null
+    rows.push({
+      id,
+      score: data.rrf,
+      type: entity.type,
+      metadata: entity.metadata,
+      textMatches:
+        textContent === null ? [] : queryWords.filter((w) => textContent.includes(w.toLowerCase())),
+      textScore: data.textScore,
+      semanticScore: data.semanticScore,
+      matchSource: data.hasText && data.hasSemantic ? 'both' : data.hasText ? 'text' : 'semantic'
+    })
+  }
+
+  // The metadata intersection — after the legs, as it was.
+  if (preResolvedMetadataIds && preResolvedFilter) {
+    const filteredIdSet = new Set(preResolvedMetadataIds)
+    rows = rows.filter((r) => filteredIdSet.has(r.id))
+  }
+  if (graphFirstIds !== null) {
+    const neighbourSet = new Set(graphFirstIds)
+    rows = rows.filter((r) => neighbourSet.has(r.id))
+  }
+
+  // Rank to the page, then cut it.
+  const order = rankIndicesByScore(
+    rows.map((r) => r.score),
+    offset + limit,
+    true
+  )
+  return reorderByIndices(rows, order).slice(offset, offset + limit)
+}
+
+/**
+ * FIXTURE A — the filter's universe covers every text match, so the two orders
+ * rank exactly the same rows and the answers must be identical.
+ */
+describe('hybrid find: filter before hydrate — the answer is unchanged', () => {
+  let brain: Brainy<any>
+  const QUERY = 'orbital telemetry'
+  const MATCHES = 24
+  const FILLER = 120
+  const OUTSIDE = 30
+  const VFS = 10
+  const RETRACTED = 6
+  const anchor = 'array-anchor'
+  const matchIds: string[] = []
+
+  beforeAll(async () => {
+    brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+
+    let seed = 1
+    await brain.add({
+      id: anchor,
+      data: 'ground station anchor record',
+      type: NounType.Thing,
+      metadata: { lane: 'alpha', role: 'anchor' },
+      vector: seededVector(seed++)
+    })
+
+    // Rows the query's words actually match — all inside every filter below.
+    for (let i = 0; i < MATCHES; i++) {
+      const id = `match-${i}`
+      await brain.add({
+        id,
+        data: `orbital telemetry packet ${i} recorded downlink`,
+        type: NounType.Document,
+        metadata: { lane: 'alpha', rank: i },
+        vector: seededVector(seed++)
+      })
+      matchIds.push(resolveEntityId(id))
+      await brain.relate({ from: anchor, to: id, type: VerbType.RelatedTo })
+    }
+    // Rows inside the universe that the query's words do NOT match.
+    for (let i = 0; i < FILLER; i++) {
+      await brain.add({
+        id: `filler-${i}`,
+        data: `cistern ledger entry ${i} archived`,
+        type: NounType.Document,
+        metadata: { lane: 'alpha', rank: 1000 + i },
+        vector: seededVector(seed++)
+      })
+    }
+    // Rows outside the universe.
+    for (let i = 0; i < OUTSIDE; i++) {
+      await brain.add({
+        id: `outside-${i}`,
+        data: `unrelated dossier ${i}`,
+        type: NounType.Person,
+        metadata: { lane: 'beta' },
+        vector: seededVector(seed++)
+      })
+    }
+    // VFS infrastructure rows — excluded by excludeVFS.
+    for (let i = 0; i < VFS; i++) {
+      await brain.add({
+        id: `vfs-${i}`,
+        data: `mounted path ${i}`,
+        type: NounType.Document,
+        metadata: { lane: 'alpha', vfsType: 'file' },
+        vector: seededVector(seed++)
+      })
+    }
+    // Retracted rows — excluded by a `missing` negation.
+    for (let i = 0; i < RETRACTED; i++) {
+      await brain.add({
+        id: `retracted-${i}`,
+        data: `withdrawn note ${i}`,
+        type: NounType.Document,
+        metadata: { lane: 'alpha', retracted: true },
+        vector: seededVector(seed++)
+      })
+    }
+
+    // The reference index has no opaque-set door, so the pipeline and the
+    // oracle both restrict the beam walk with the materialized candidate ids.
+    expect(typeof (brain as any).metadataIndex.getIdSetForFilter).not.toBe('function')
+  })
+
+  it('the fixture does not truncate the text leg — the universe covers every text match', async () => {
+    const index = (brain as any).metadataIndex
+    const textMatches = await index.getIdsForTextQuery(QUERY)
+    expect(textMatches).toHaveLength(MATCHES)
+    const universe = await (brain as any).filterIdsBelted({ lane: 'alpha' })
+    const inUniverse = new Set(universe)
+    for (const m of textMatches) expect(inUniverse.has(m.id)).toBe(true)
+  })
+
+  it('hybrid + where: identical rows, identical order, identical scores', async () => {
+    const params = { query: QUERY, where: { lane: 'alpha' }, limit: 8 }
+    const expected = await legacyHybridFind(brain as any, params)
+    const actual = await brain.find(params as any)
+    expect(actual.length).toBe(expected.length)
+    expect(project(actual)).toEqual(expected)
+  })
+
+  it('hybrid + where + offset: identical page two', async () => {
+    const params = { query: QUERY, where: { lane: 'alpha' }, limit: 6, offset: 6 }
+    const expected = await legacyHybridFind(brain as any, params)
+    const actual = await brain.find(params as any)
+    expect(actual.length).toBe(expected.length)
+    expect(project(actual)).toEqual(expected)
+  })
+
+  it('hybrid + type list + excludeVFS + a `missing` negation: identical', async () => {
+    const params = {
+      query: QUERY,
+      type: [NounType.Document, NounType.Person],
+      excludeVFS: true,
+      where: { lane: 'alpha', retracted: { missing: true } },
+      limit: 8
+    }
+    const expected = await legacyHybridFind(brain as any, params)
+    const actual = await brain.find(params as any)
+    expect(actual.length).toBe(expected.length)
+    expect(project(actual)).toEqual(expected)
+    for (const r of actual) {
+      expect(r.metadata.retracted).toBeUndefined()
+      expect(r.metadata.vfsType).toBeUndefined()
+    }
+  })
+
+  it('hybrid + type list + excludeVFS + a `missing` negation, offset: identical', async () => {
+    const params = {
+      query: QUERY,
+      type: [NounType.Document, NounType.Person],
+      excludeVFS: true,
+      where: { lane: 'alpha', retracted: { missing: true } },
+      limit: 5,
+      offset: 5
+    }
+    const expected = await legacyHybridFind(brain as any, params)
+    const actual = await brain.find(params as any)
+    expect(actual.length).toBe(expected.length)
+    expect(project(actual)).toEqual(expected)
+  })
+
+  it('hybrid + connected: identical, and never a non-neighbour', async () => {
+    const params = {
+      query: QUERY,
+      connected: { from: anchor, direction: 'out' as const },
+      where: { lane: 'alpha' },
+      limit: 8
+    }
+    const expected = await legacyHybridFind(brain as any, params)
+    const actual = await brain.find(params as any)
+    expect(actual.length).toBe(expected.length)
+    expect(project(actual)).toEqual(expected)
+    const neighbours = new Set(matchIds)
+    for (const r of actual) expect(neighbours.has(r.id)).toBe(true)
+  })
+
+  it('hybrid + connected + offset: page two is the page, not an empty answer', async () => {
+    const params = {
+      query: QUERY,
+      connected: { from: anchor, direction: 'out' as const },
+      where: { lane: 'alpha' },
+      limit: 5,
+      offset: 5
+    }
+    const expected = await legacyHybridFind(brain as any, params)
+    expect(expected).toHaveLength(5)
+    const actual = await brain.find(params as any)
+    expect(actual.length).toBe(expected.length)
+    expect(project(actual)).toEqual(expected)
+  })
+
+  it('hybrid + connected: paging reaches every matching neighbour exactly once', async () => {
+    const seen = new Set<string>()
+    for (let offset = 0; offset < MATCHES; offset += 6) {
+      const page = await brain.find({
+        query: QUERY,
+        connected: { from: anchor, direction: 'out' as const },
+        where: { lane: 'alpha' },
+        limit: 6,
+        offset
+      } as any)
+      for (const r of page) {
+        expect(seen.has(r.id)).toBe(false)
+        seen.add(r.id)
+      }
+    }
+    // Every row the fused candidate set holds is reachable by paging, and the
+    // neighbour set is the ceiling.
+    expect(seen.size).toBeGreaterThanOrEqual(MATCHES)
+    const neighbours = new Set(matchIds)
+    for (const id of seen) expect(neighbours.has(id)).toBe(true)
+  })
+
+  it('hybrid + fusion + offset: page two is the page', async () => {
+    const plain = await brain.find({
+      query: QUERY,
+      where: { lane: 'alpha' },
+      limit: 5,
+      offset: 5
+    } as any)
+    const fused = await brain.find({
+      query: QUERY,
+      where: { lane: 'alpha' },
+      fusion: 'weighted',
+      limit: 5,
+      offset: 5
+    } as any)
+    expect(fused).toHaveLength(plain.length)
+    expect(fused.map((r) => r.id)).toEqual(plain.map((r) => r.id))
+  })
+
+  it('a hydrated hybrid row is shaped exactly as an eagerly-built one', async () => {
+    const rows = await brain.find({ query: QUERY, where: { lane: 'alpha' }, limit: 8 } as any)
+    const row = rows[0]
+    expect(Object.keys(row)).toEqual([
+      'id',
+      'score',
+      'type',
+      'subtype',
+      'visibility',
+      'metadata',
+      'data',
+      'confidence',
+      'weight',
+      '_rev',
+      'entity',
+      'textMatches',
+      'textScore',
+      'semanticScore',
+      'matchSource'
+    ])
+    // The flattened fields are projections of the entity, as always.
+    expect(row.entity).toBeDefined()
+    expect(row.type).toBe(row.entity.type)
+    expect(row.metadata).toBe(row.entity.metadata)
+    expect(row.data).toBe(row.entity.data)
+    expect(row._rev).toBe(row.entity._rev)
+    // The match visibility survives the deferral — every leg's fields, on the
+    // rows that leg contributed, exactly as the eager pipeline set them.
+    expect(['text', 'semantic', 'both']).toContain(row.matchSource)
+    for (const r of rows) {
+      if (r.matchSource === 'semantic') {
+        expect(r.textMatches).toEqual([])
+        expect(r.textScore).toBeUndefined()
+      } else {
+        expect(r.textMatches).toEqual(['orbital', 'telemetry'])
+        expect(typeof r.textScore).toBe('number')
+      }
+      if (r.matchSource === 'text') {
+        expect(r.semanticScore).toBeUndefined()
+      } else {
+        expect(typeof r.semanticScore).toBe('number')
+      }
+    }
+  })
+
+  it('reads canonical for the page only — one batch, `limit` rows', async () => {
+    // Warm any first-read verification before the counters are read.
+    await brain.find({ query: QUERY, where: { lane: 'alpha' }, limit: 1 } as any)
+
+    const hydrate = vi.spyOn(brain as any, 'batchGet')
+    try {
+      const results = await brain.find({ query: QUERY, where: { lane: 'alpha' }, limit: 10 } as any)
+      expect(results).toHaveLength(10)
+      expect(hydrate).toHaveBeenCalledTimes(1)
+      expect((hydrate.mock.calls[0][0] as string[]).length).toBe(10)
+    } finally {
+      hydrate.mockRestore()
+    }
+  })
+
+  it('asks the text index about the universe only, never the whole store', async () => {
+    const index = (brain as any).metadataIndex
+    const wholeStore = vi.spyOn(index, 'getIdsForTextQuery')
+    const within = vi.spyOn(index, 'getIdsForTextQueryWithin')
+    try {
+      await brain.find({ query: QUERY, where: { lane: 'alpha' }, limit: 10 } as any)
+      expect(wholeStore).not.toHaveBeenCalled()
+      expect(within).toHaveBeenCalledTimes(1)
+
+      const askedIds = within.mock.calls[0][1] as string[]
+      const universe = await (brain as any).filterIdsBelted({ lane: 'alpha' })
+      expect(askedIds).toHaveLength(universe.length)
+
+      // What the text leg marshals is bounded by the universe, not the store.
+      const marshalled = (await within.mock.results[0].value) as unknown[]
+      expect(marshalled.length).toBeLessThanOrEqual(universe.length)
+      expect(marshalled).toHaveLength(MATCHES)
+    } finally {
+      wholeStore.mockRestore()
+      within.mockRestore()
+    }
+  })
+
+  it('the two text doors agree: within is the whole-store answer restricted', async () => {
+    const index = (brain as any).metadataIndex
+    const universe: string[] = await (brain as any).filterIdsBelted({
+      lane: 'alpha',
+      retracted: { missing: true }
+    })
+    const inUniverse = new Set(universe)
+    const whole = await index.getIdsForTextQuery(QUERY)
+    const within = await index.getIdsForTextQueryWithin(QUERY, universe)
+    expect(within).toEqual(whole.filter((m: any) => inUniverse.has(m.id)))
+    expect(await index.getIdsForTextQueryWithin(QUERY, [])).toEqual([])
+  })
+})
+
+/**
+ * FIXTURE B — the query's words are common OUTSIDE the universe, so the old
+ * order's text leg was entirely consumed by rows the filter then discarded.
+ * This is the corrected behaviour, held by name.
+ */
+describe('hybrid find: the text leg ranks inside the filter, not around it', () => {
+  let brain: Brainy<any>
+  const QUERY = 'orbital telemetry drift'
+  const NOISE = 150
+  const KEEP = 15
+  const keepIds: string[] = []
+
+  beforeAll(async () => {
+    brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+
+    let seed = 5000
+    // Added FIRST and matching one more query word, so they lead the
+    // store-wide text ranking outright — and none of them pass the filter.
+    for (let i = 0; i < NOISE; i++) {
+      await brain.add({
+        id: `noise-${i}`,
+        data: `orbital telemetry drift report ${i}`,
+        type: NounType.Document,
+        metadata: { lane: 'beta' },
+        vector: seededVector(seed++)
+      })
+    }
+    for (let i = 0; i < KEEP; i++) {
+      const id = `keep-${i}`
+      await brain.add({
+        id,
+        data: `orbital telemetry summary ${i}`,
+        type: NounType.Document,
+        metadata: { lane: 'alpha' },
+        vector: seededVector(seed++)
+      })
+      keepIds.push(resolveEntityId(id))
+    }
+  })
+
+  it('the old order let the filter consume the whole text leg', async () => {
+    const index = (brain as any).metadataIndex
+    const universe: string[] = await (brain as any).filterIdsBelted({ lane: 'alpha' })
+    expect(universe).toHaveLength(KEEP)
+    const inUniverse = new Set(universe)
+
+    // The store-wide prefix the old text leg took (limit 10 → limit * 4).
+    const prefix = (await index.getIdsForTextQuery(QUERY)).slice(0, 40)
+    expect(prefix).toHaveLength(40)
+    expect(prefix.filter((m: any) => inUniverse.has(m.id))).toHaveLength(0)
+
+    // Every row the old text leg ranked was then discarded by the filter, so
+    // the old answer carried NO text contribution at all — fifteen rows that
+    // match the query's words exactly, and not one of them reached the page
+    // through the text leg. What the old order returned was whatever the
+    // semantic leg alone happened to reach.
+    const legacy = await legacyHybridFind(brain as any, {
+      query: QUERY,
+      where: { lane: 'alpha' },
+      limit: 10
+    })
+    for (const r of legacy) {
+      expect(r.matchSource).toBe('semantic')
+      expect(r.textScore).toBeUndefined()
+      expect(r.textMatches).toEqual([])
+    }
+  })
+
+  it('the new order ranks the text leg inside the universe', async () => {
+    const results = await brain.find({
+      query: QUERY,
+      where: { lane: 'alpha' },
+      limit: 10
+    } as any)
+
+    expect(results).toHaveLength(10)
+    const keeps = new Set(keepIds)
+    for (const r of results) {
+      expect(keeps.has(r.id)).toBe(true)
+      expect(r.metadata.lane).toBe('alpha')
+      // The text leg is the contributor the old order threw away.
+      expect(['text', 'both']).toContain(r.matchSource)
+      expect(r.textScore).toBe(1)
+      expect(r.textMatches).toEqual(['orbital', 'telemetry'])
+    }
+  })
+
+  it('paging reaches every matching row the old order could not see', async () => {
+    const seen = new Set<string>()
+    for (let offset = 0; offset < KEEP; offset += 5) {
+      const page = await brain.find({
+        query: QUERY,
+        where: { lane: 'alpha' },
+        limit: 5,
+        offset
+      } as any)
+      expect(page).toHaveLength(5)
+      for (const r of page) {
+        expect(seen.has(r.id)).toBe(false)
+        seen.add(r.id)
+      }
+    }
+    expect(seen.size).toBe(KEEP)
+    expect([...seen].sort()).toEqual([...keepIds].sort())
+  })
+
+  it('reads canonical for the page only, on the truncating shape too', async () => {
+    await brain.find({ query: QUERY, where: { lane: 'alpha' }, limit: 1 } as any)
+
+    const hydrate = vi.spyOn(brain as any, 'batchGet')
+    try {
+      const results = await brain.find({ query: QUERY, where: { lane: 'alpha' }, limit: 10 } as any)
+      expect(results).toHaveLength(10)
+      expect(hydrate).toHaveBeenCalledTimes(1)
+      expect((hydrate.mock.calls[0][0] as string[]).length).toBe(10)
+    } finally {
+      hydrate.mockRestore()
+    }
+  })
+})

tests/integration/find-near.test.ts

@@ -0,0 +1,48 @@
+/**
+ * @module tests/integration/find-near
+ * @description find({ near }) searches around the anchor's OWN vector (10.4.10).
+ *
+ * The proximity search fetched its anchor without vectors and fed a
+ * zero-length vector to the index — every near() refused with a dimension
+ * mismatch, for every caller. Found by the Rust planner's first-contact pins
+ * (the planner declines `near`; the pin compared outcomes with and without
+ * it). Now the anchor is fetched with its vector, and an anchor without one
+ * refuses by name instead of failing inside the index.
+ */
+import { describe, it, expect, beforeAll } from 'vitest'
+import { Brainy } from '../../src/brainy'
+import { NounType } from '../../src/types/graphTypes'
+import { v5 } from '../../src/universal/uuid'
+import { generateTestVector } from '../helpers/test-factory'
+
+describe('find({ near }) uses the anchor vector', () => {
+  let brain: Brainy<any>
+  const anchorVector = generateTestVector()
+
+  beforeAll(async () => {
+    brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+    await brain.add({ id: 'anchor', data: 'anchor row', type: NounType.Thing, vector: anchorVector })
+    // A twin with the identical vector and a far row.
+    await brain.add({ id: 'twin', data: 'twin row', type: NounType.Thing, vector: [...anchorVector] })
+    await brain.add({ id: 'far', data: 'far row', type: NounType.Thing, vector: generateTestVector() })
+  })
+
+  it('returns the anchor\'s neighbours by its own vector', async () => {
+    const results = await brain.find({ near: { id: 'anchor' }, limit: 3 })
+    expect(results.length).toBeGreaterThan(0)
+    const ids = results.map((r) => r.entity.id)
+    expect(ids).toContain(v5('twin'))
+  })
+
+  it('refuses by name when the anchor has no vector', async () => {
+    await brain.add({
+      id: 'unvectored',
+      data: 'no vector here',
+      type: NounType.Thing,
+      deferEmbedding: true
+    })
+    ;(brain as any).kickEmbedWorker = () => {}
+    await expect(brain.find({ near: { id: 'unvectored' }, limit: 3 })).rejects.toThrow(/has no vector to search around/)
+  })
+})

tests/integration/find-planner-door.test.ts

@@ -0,0 +1,137 @@
+/**
+ * @module tests/integration/find-planner-door
+ * @description The optional `MetadataIndexProvider.planFindPage` door.
+ *
+ * The stage doors each serve one stage, so a `find()` that consults three of
+ * them crosses into the index three times and marshals a result set at every
+ * crossing — a filter matching a hundred thousand rows builds a hundred
+ * thousand id strings to return a page of twenty-five. An index that can decide
+ * the stage order itself answers the page in one call.
+ *
+ * These pins hold the three properties that make such a door safe to add:
+ *
+ * 1. **Absent, nothing changes.** The reference index has no planner, and every
+ *    find is served by the stage doors exactly as before. That is also what
+ *    makes this engine the ordering oracle for any index that implements one.
+ * 2. **Present, it is asked first and its answer is used** — above the branch
+ *    selection, with the params already normalized, the hidden ids passed, and
+ *    the graph provider handed over.
+ * 3. **`null` is routing, not an answer.** A door that declines a shape leaves
+ *    it to the path that always served it, and the result is unchanged.
+ *
+ * Plus the serving law: an empty page stamped `emptyAt: 'graph'` is re-verified
+ * against the adjacency before it is believed, so a not-serving graph refuses
+ * loudly instead of answering `[]` as truth.
+ */
+import { describe, it, expect, beforeAll, vi } from 'vitest'
+import { Brainy } from '../../src/brainy'
+import { NounType, VerbType } from '../../src/types/graphTypes'
+import { generateTestVector } from '../helpers/test-factory'
+
+describe('find(): the optional planner door', () => {
+  let brain: Brainy<any>
+  const anchor = 'planner-anchor'
+  let neighbourId = ''
+
+  beforeAll(async () => {
+    brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+    await brain.add({
+      id: anchor,
+      data: 'anchor',
+      type: NounType.Person,
+      metadata: { kind: 'anchor' },
+      vector: generateTestVector()
+    })
+    for (let i = 0; i < 12; i++) {
+      const id = await brain.add({
+        id: `row-${i}`,
+        data: `row ${i}`,
+        type: NounType.Person,
+        metadata: { kind: 'note', rank: i },
+        vector: generateTestVector()
+      })
+      if (i === 0) neighbourId = id
+      await brain.relate({ from: anchor, to: id, type: VerbType.Knows })
+    }
+  })
+
+  /** Install a planner door for one call, then remove it. */
+  const withDoor = async <T>(
+    door: (...a: any[]) => Promise<any>,
+    body: () => Promise<T>
+  ): Promise<T> => {
+    const index = (brain as any).metadataIndex
+    index.planFindPage = door
+    try {
+      return await body()
+    } finally {
+      delete index.planFindPage
+    }
+  }
+
+  it('is absent on the reference index — every find is served by the stage doors', async () => {
+    expect((brain as any).metadataIndex.planFindPage).toBeUndefined()
+    const results = await brain.find({ where: { kind: 'note' }, limit: 5 })
+    expect(results).toHaveLength(5)
+  })
+
+  it('is asked before the branches, with normalized params and the graph provider', async () => {
+    const door = vi.fn(async () => null)
+    await withDoor(door, async () => {
+      await brain.find({ where: { kind: 'note' }, limit: 5 })
+    })
+    expect(door).toHaveBeenCalledTimes(1)
+    const [params, hidden, graph] = door.mock.calls[0] as any[]
+    expect(params.where).toEqual({ kind: 'note' })
+    expect(Array.isArray(hidden)).toBe(true)
+    expect(graph).toBe((brain as any).graphIndex)
+  })
+
+  it('uses the page it answers, hydrated and in the door\'s order', async () => {
+    const results = await withDoor(
+      async () => ({ ids: [neighbourId], emptyAt: 'none' as const }),
+      async () => brain.find({ where: { kind: 'note' }, limit: 5 })
+    )
+    expect(results).toHaveLength(1)
+    expect(results[0].entity.id).toBe(neighbourId)
+  })
+
+  it('a declining door changes nothing — the shape is served as it always was', async () => {
+    const withoutDoor = await brain.find({ where: { kind: 'note' }, orderBy: 'rank', limit: 4 })
+    const declined = await withDoor(
+      async () => null,
+      async () => brain.find({ where: { kind: 'note' }, orderBy: 'rank', limit: 4 })
+    )
+    expect(declined.map((r) => r.entity.id)).toEqual(withoutDoor.map((r) => r.entity.id))
+  })
+
+  it('re-verifies the adjacency before believing an empty graph answer', async () => {
+    const verify = vi.spyOn(brain as any, 'verifyGraphAdjacencyLive')
+    try {
+      const results = await withDoor(
+        async () => ({ ids: [], emptyAt: 'graph' as const }),
+        async () => brain.find({ connected: { from: anchor }, where: { kind: 'note' }, limit: 5 })
+      )
+      expect(results).toEqual([])
+      expect(verify).toHaveBeenCalled()
+    } finally {
+      verify.mockRestore()
+    }
+  })
+
+  it('does not re-verify the adjacency for an empty the FILTER produced', async () => {
+    const verify = vi.spyOn(brain as any, 'verifyGraphAdjacencyLive')
+    verify.mockClear()
+    try {
+      const results = await withDoor(
+        async () => ({ ids: [], emptyAt: 'filter' as const }),
+        async () => brain.find({ where: { kind: 'note' }, limit: 5 })
+      )
+      expect(results).toEqual([])
+      expect(verify).not.toHaveBeenCalled()
+    } finally {
+      verify.mockRestore()
+    }
+  })
+})

tests/integration/generation-store-factory.test.ts

@@ -0,0 +1,101 @@
+/**
+ * @module tests/integration/generation-store-factory
+ * @description Pins the `createGenerationStore` protected factory hook on
+ * `Brainy` ({@link Brainy.createGenerationStore}). The hook exists so an
+ * engine built on top of this reference implementation can substitute a
+ * `GenerationStore` that keeps the same behavioural contract; this suite
+ * proves two things:
+ *
+ *  1. A subclass overriding the hook is the ONLY path that constructs the
+ *     generation store — it is called exactly once, with the same storage
+ *     instance `performInit` holds — and the store the brain actually uses
+ *     is the one the override returned.
+ *  2. The default (non-overridden) path is unaffected — proven here by
+ *     confirming the base class still produces a plain `GenerationStore`
+ *     wired to `brain.storage`, and separately by running the existing
+ *     `db-mvcc` and `brainy-core.integration` suites unmodified against this
+ *     change (they exercise generation-store behaviour end to end).
+ */
+
+import { describe, it, expect, afterEach } from 'vitest'
+import { Brainy } from '../../src/brainy.js'
+import { GenerationStore } from '../../src/db/generationStore.js'
+import type { BaseStorage } from '../../src/storage/baseStorage.js'
+
+/** Typed access to the brain's private storage + generation-store fields (test injection point). */
+function internalsOf(brain: Brainy): { storage: BaseStorage; generationStore: GenerationStore } {
+  return brain as unknown as { storage: BaseStorage; generationStore: GenerationStore }
+}
+
+/**
+ * A `GenerationStore` subclass that counts its own construction and
+ * remembers the storage instance it was built with, so the test can prove
+ * the hook is the sole construction path without mocking the module.
+ */
+class SpyGenerationStore extends GenerationStore {
+  static constructCount = 0
+  static lastStorage: BaseStorage | undefined
+
+  constructor(storage: BaseStorage) {
+    super(storage)
+    SpyGenerationStore.constructCount++
+    SpyGenerationStore.lastStorage = storage
+  }
+}
+
+/** A Brainy subclass overriding the factory hook — stands in for an engine built on the reference. */
+class BrainyWithSpyStore extends Brainy {
+  hookCallCount = 0
+  hookStorageArg: BaseStorage | undefined
+
+  protected override createGenerationStore(storage: BaseStorage): GenerationStore {
+    this.hookCallCount++
+    this.hookStorageArg = storage
+    return new SpyGenerationStore(storage)
+  }
+}
+
+describe('Brainy.createGenerationStore — protected factory hook', () => {
+  const brains: Brainy[] = []
+
+  afterEach(async () => {
+    SpyGenerationStore.constructCount = 0
+    SpyGenerationStore.lastStorage = undefined
+    for (const brain of brains.splice(0)) {
+      try {
+        await brain.close()
+      } catch {
+        // already closed by the test
+      }
+    }
+  })
+
+  it('a subclass override is the sole construction path: called once, same storage instance, its store is the one the brain uses', async () => {
+    const brain = new BrainyWithSpyStore({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+    brains.push(brain)
+
+    // Called exactly once, through the hook.
+    expect(brain.hookCallCount).toBe(1)
+    expect(SpyGenerationStore.constructCount).toBe(1)
+
+    // Same storage instance the base class holds — not a copy, not a different adapter.
+    const { storage, generationStore } = internalsOf(brain)
+    expect(brain.hookStorageArg).toBe(storage)
+    expect(SpyGenerationStore.lastStorage).toBe(storage)
+
+    // The store the brain actually uses is the one the override returned.
+    expect(generationStore).toBeInstanceOf(SpyGenerationStore)
+  })
+
+  it('the default (non-overridden) path still produces a plain GenerationStore wired to the same storage', async () => {
+    const brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+    brains.push(brain)
+
+    const { storage, generationStore } = internalsOf(brain)
+    expect(generationStore).toBeInstanceOf(GenerationStore)
+    // The default implementation constructs from the same storage the brain holds.
+    expect((generationStore as unknown as { storage: BaseStorage }).storage).toBe(storage)
+  })
+})

tests/integration/history-repacking.test.ts

@@ -16,6 +16,7 @@ import { describe, it, expect, afterEach } from 'vitest'
 import * as fs from 'node:fs'
 import * as path from 'node:path'
 import * as os from 'node:os'
+import * as zlib from 'node:zlib'
 import { Brainy } from '../../src/brainy.js'
 import { NounType } from '../../src/types/graphTypes.js'
 import { GenerationStore } from '../../src/db/generationStore.js'
@@ -57,6 +58,107 @@ describe('history repacking — the two-tier lifecycle', () => {
     }
   })
 
+  /**
+   * THE HOLE, END TO END — the shape a real store carries.
+   *
+   * A forensic fixture was measured with generation directories 1..2503
+   * present except for exactly one: 1416. Its fact-log segment already showed
+   * the tell — `seg-...1410.bfl` declaring firstGeneration 1410, lastGeneration
+   * 1940 (531 generations) while recording only 530 facts.
+   *
+   * Before the fix, repacking such a store folded ACROSS that hole: the batch
+   * skipped 1416 (no readable delta) and the sealed segment declared a range
+   * spanning it anyway. The next open merged that declared range back into
+   * committedRanges, re-admitting 1416 as committed history, and every
+   * subsequent auto-compaction pass then asked the packed tier for a frame
+   * that was never written — producing, on EVERY run, the non-fatal narration
+   *
+   *   Auto-compaction of generational history failed (non-fatal): generation
+   *   N is inside sealed segment seg-....bgs's declared range but has no frame
+   *   — packed history is damaged
+   *
+   * This pin removes a generation directory to make the same hole, then
+   * requires repack + reopen + compaction to complete cleanly.
+   */
+  it('a missing generation directory does not poison the packed tier', async () => {
+    const dir = tempDir()
+    // `retention: 'all'` throughout: close() otherwise auto-compacts the
+    // history away, and this pin needs the cold generations still on disk so
+    // there is something to punch a hole in. The live window stays at its
+    // production default for the build phase, so nothing folds yet.
+    const archival = async (): Promise<Brainy> => {
+      const b = new Brainy({
+        requireSubtype: false,
+        storage: { type: 'filesystem', path: dir },
+        embeddingFunction: stub,
+        retention: 'all'
+      })
+      await b.init()
+      return b
+    }
+    const brain = await archival()
+
+    const id = await brain.add({
+      data: 'holed-entity',
+      type: NounType.Document,
+      metadata: { v: 0 }
+    })
+    // One flush per update: single-op writes coalesce inside a flush window,
+    // so a history deep enough to have a middle needs the windows separated.
+    for (let v = 1; v <= 12; v++) {
+      await brain.update({ id, metadata: { v } })
+      await brain.flush()
+    }
+    await brain.close()
+
+    // Punch the hole: delete ONE generation directory in the middle of the
+    // cold range, exactly as the real store presents it.
+    const genRoot = path.join(dir, '_generations')
+    const numeric = fs
+      .readdirSync(genRoot, { withFileTypes: true })
+      .filter((e) => e.isDirectory() && /^\d+$/.test(e.name))
+      .map((e) => Number(e.name))
+      .sort((a, b) => a - b)
+    expect(numeric.length).toBeGreaterThan(6)
+    const victim = numeric[Math.floor(numeric.length / 2)]
+    fs.rmSync(path.join(genRoot, String(victim)), { recursive: true, force: true })
+
+    // Now shrink the live window and reopen. close() repacks automatically
+    // (brainy.ts phase 0b), so this is the production sequence exactly: a
+    // store with a hole in its history gets folded by ordinary housekeeping,
+    // with nobody asking for it.
+    ;(GenerationStore as any).REPACK_LIVE_WINDOW = 3
+    const reopened = await archival()
+    const result = await reopened.repackHistory()
+    expect(result.foldedGenerations).toBeGreaterThan(0)
+
+    const segDir = path.join(dir, SEGMENTS_PREFIX)
+    const manifestPath = ['manifest.json', 'manifest.json.gz']
+      .map((f) => path.join(segDir, f))
+      .find((p) => fs.existsSync(p))!
+    const raw = manifestPath.endsWith('.gz')
+      ? zlib.gunzipSync(fs.readFileSync(manifestPath)).toString('utf8')
+      : fs.readFileSync(manifestPath, 'utf8')
+    const manifest = JSON.parse(raw) as {
+      segments: Array<{ firstGeneration: number; lastGeneration: number; frames: number }>
+    }
+
+    // THE LAW: every sealed segment declares exactly as many generations as it
+    // holds frames, and none of them spans the victim.
+    for (const s of manifest.segments) {
+      expect(s.lastGeneration - s.firstGeneration + 1).toBe(s.frames)
+      expect(victim >= s.firstGeneration && victim <= s.lastGeneration).toBe(false)
+    }
+
+    await reopened.close()
+
+    // And the pass that used to fail on every run now completes: reopen (which
+    // re-seeds committedRanges from the packed tier) then compact history.
+    const third = await openBrain(dir)
+    await expect(third.compactHistory({ maxGenerations: 2 })).resolves.toBeDefined()
+    await third.close()
+  })
+
   it('repack preserves every historical read across cold reopen; folded dirs are gone', async () => {
     ;(GenerationStore as any).REPACK_LIVE_WINDOW = 3
     const dir = tempDir()

tests/integration/pending-embed-checkpoint.test.ts

@@ -0,0 +1,547 @@
+/**
+ * @module tests/integration/pending-embed-checkpoint
+ * @description THE PENDING-EMBED CHECKPOINT — the bound that engages on the
+ * brains that need it.
+ *
+ * 10.4.9 bounded the open-path `recover-pending-embeds` fold with a LOW-WATER
+ * MARK: the log head at which the pending set last drained to EMPTY. That mark
+ * carries no set, so it can only be written when the set is empty — and a brain
+ * holding even ONE id that never lands (an embed that keeps failing, a worker
+ * that never gets to it, a row reaped in memory only and re-folded every open)
+ * never drains, therefore never writes a mark, therefore re-reads its WHOLE
+ * fact log on every single open. The bound was absent from exactly the brains
+ * whose fold is expensive: a silent scaling defect.
+ *
+ * The cure is a CHECKPOINT of the pending set —
+ * `_system/pending_embeds_checkpoint.json` = `{ generation, pending, writtenAt }`,
+ * meaning "as of durable generation G the pending set was exactly this list".
+ * Open seeds the set from `pending` and scans only from `G + 1`, so the fold is
+ * O(facts since G) whether or not the set ever drains.
+ *
+ * What this suite pins:
+ *   1. A brain with one permanently-stuck pending id, closed cleanly and
+ *      reopened, scans ONLY the facts after the checkpoint — asserted from the
+ *      fold's own accounting, never a clock. The same fixture pins the DEFECT:
+ *      no low-water mark exists on that brain, because it never drained.
+ *   2. A crash matrix in a REAL child process (SIGKILL, no close), for kills
+ *      before a checkpoint write, after one with embeds landed and flushed
+ *      after it, and after one with an UN-FLUSHED tail at the moment of death.
+ *      The invariant in every row is differential: the checkpoint-bounded fold
+ *      the reopened brain actually ran ≡ a full fold from generation 1 over the
+ *      same recovered log.
+ *   3. A torn checkpoint falls back — loudly (the adapter's torn-record gauge
+ *      plus the fold's own narration of which bound applied) and correctly.
+ *   4. The existing low-water pins keep passing unchanged
+ *      (`pending-embed-low-water.test.ts`): the mark is still written and is
+ *      still read, now as the FALLBACK bound beneath the checkpoint.
+ *
+ * The crash-recovery contract is untouched: the fold runs on the open's
+ * foreground, so a reopened brain has its markers re-armed when open() returns.
+ */
+import { describe, it, expect, afterEach } from 'vitest'
+import { mkdtempSync, rmSync, existsSync, readFileSync, writeFileSync } from 'node:fs'
+import { spawn } from 'node:child_process'
+import { gunzipSync } from 'node:zlib'
+import { tmpdir } from 'node:os'
+import { join } from 'node:path'
+import { Brainy } from '../../src/brainy.js'
+import { NounType } from '../../src/types/graphTypes.js'
+import { getTornRecordGauge } from '../../src/storage/tornRecordError.js'
+
+const CHECKPOINT_PATH = '_system/pending_embeds_checkpoint.json'
+const LOWWATER_PATH = '_system/pending_embeds_lowwater.json'
+const REPO_ROOT = process.cwd()
+const TSX = join(REPO_ROOT, 'node_modules', '.bin', 'tsx')
+
+/** The fold's own accounting for the most recent open. */
+interface FoldReport {
+  bound: 'checkpoint' | 'low-water' | 'genesis'
+  fromGeneration: number
+  factsScanned: number
+  seeded: number
+  pending: number
+}
+
+const roots: string[] = []
+const liveBrains: Brainy<any>[] = []
+
+function dir(): string {
+  const d = mkdtempSync(join(tmpdir(), 'brainy-embed-ckpt-'))
+  roots.push(d)
+  return d
+}
+
+async function open(root: string, opts?: { blockWorker?: boolean }): Promise<Brainy<any>> {
+  const brain = new Brainy<any>({
+    requireSubtype: false,
+    storage: { type: 'filesystem', path: root }
+  })
+  // Blocking the worker BEFORE init() is how a "permanently stuck" pending id
+  // is built deterministically: the state under test is "an id the fold keeps
+  // re-arming and nothing ever disarms", and its production causes (a failing
+  // embedder, a wedged model, a data-less row) all reduce to exactly that.
+  if (opts?.blockWorker) (brain as unknown as { kickEmbedWorker: () => void }).kickEmbedWorker = () => {}
+  await brain.init()
+  liveBrains.push(brain)
+  return brain
+}
+
+function foldReport(brain: Brainy<any>): FoldReport {
+  const report = (brain as unknown as { _pendingEmbedFoldReport: FoldReport | null })
+    ._pendingEmbedFoldReport
+  if (report === null) throw new Error('the open ran no pending-embed fold')
+  return report
+}
+
+function pendingIds(brain: Brainy<any>): string[] {
+  return [
+    ...(brain as unknown as { _pendingEmbedIds: Set<string> })._pendingEmbedIds
+  ].sort()
+}
+
+/** Read an artifact straight off disk (the adapter gzips raw objects). */
+function readArtifact(root: string, path: string): Record<string, unknown> | null {
+  const plain = join(root, ...path.split('/'))
+  const gz = `${plain}.gz`
+  if (existsSync(gz)) return JSON.parse(gunzipSync(readFileSync(gz)).toString('utf-8'))
+  if (existsSync(plain)) return JSON.parse(readFileSync(plain, 'utf-8'))
+  return null
+}
+
+/** The on-disk path the adapter actually used for an artifact. */
+function artifactPath(root: string, path: string): string | null {
+  const plain = join(root, ...path.split('/'))
+  const gz = `${plain}.gz`
+  if (existsSync(gz)) return gz
+  if (existsSync(plain)) return plain
+  return null
+}
+
+/**
+ * THE DIFFERENTIAL ORACLE: fold the log from generation 1 with exactly the
+ * engine's own rules. This is what the bounded fold must agree with, and its
+ * fact count is what the unbounded fold used to read at every open.
+ */
+async function fullFold(brain: Brainy<any>): Promise<{ ids: string[]; facts: number }> {
+  const log = (
+    brain as unknown as { generationStore: { getFactLog(): any } }
+  ).generationStore.getFactLog()
+  const pending = new Set<string>()
+  let facts = 0
+  const scan = log.scanFacts({ fromGeneration: 1 })
+  for await (const batch of scan.batches()) {
+    for (const fact of batch.facts) {
+      facts++
+      for (const record of fact.records ?? []) {
+        if (record.type === 'embed.pending') pending.add(record.id)
+        else if (record.type === 'embed.landed') pending.delete(record.id)
+      }
+      for (const op of fact.ops) {
+        if (op.kind === 'noun' && op.record === null) pending.delete(op.id)
+      }
+    }
+  }
+  return { ids: [...pending].sort(), facts }
+}
+
+/** Capture every console.warn/error line emitted while `fn` runs. */
+async function captureConsole<T>(fn: () => Promise<T>): Promise<{ result: T; lines: string[] }> {
+  const lines: string[] = []
+  const origWarn = console.warn
+  const origError = console.error
+  const sink = (...args: unknown[]) => {
+    lines.push(args.map((a) => String(a)).join(' '))
+  }
+  console.warn = sink as typeof console.warn
+  console.error = sink as typeof console.error
+  try {
+    const result = await fn()
+    return { result, lines }
+  } finally {
+    console.warn = origWarn
+    console.error = origError
+  }
+}
+
+/**
+ * Run a child process that arranges a store and then waits forever, so the
+ * parent can SIGKILL it. A real process death is the only honest way to pin
+ * "no close ran, no shutdown hook ran, RAM is gone".
+ *
+ * `detached` puts the child in its own process GROUP: tsx runs the script in a
+ * grandchild, and only a group-wide signal reaches the process holding the
+ * writer lock.
+ */
+function spawnArranger(root: string, body: string): Promise<{
+  child: ReturnType<typeof spawn>
+  output: () => string
+}> {
+  const scriptPath = join(root, 'arrange.mts')
+  writeFileSync(scriptPath, body)
+  const child = spawn(TSX, [scriptPath], {
+    cwd: REPO_ROOT,
+    stdio: ['ignore', 'pipe', 'pipe'],
+    detached: true
+  })
+  let out = ''
+  child.stdout!.on('data', (d) => { out += String(d) })
+  child.stderr!.on('data', (d) => { out += String(d) })
+  return new Promise((resolvePromise, rejectPromise) => {
+    const timer = setTimeout(
+      () => rejectPromise(new Error(`arranger never became READY:\n${out}`)),
+      180_000
+    )
+    child.stdout!.on('data', () => {
+      if (out.includes('READY')) {
+        clearTimeout(timer)
+        resolvePromise({ child, output: () => out })
+      }
+    })
+    child.on('exit', (code) => {
+      clearTimeout(timer)
+      if (!out.includes('READY')) rejectPromise(new Error(`arranger exited ${code}:\n${out}`))
+    })
+  })
+}
+
+/** Parse the `IDS:{...}` line an arranger prints — supplied ids are normalised
+ *  to canonical uuids, and the markers, checkpoint and fold all speak those. */
+function childIds(output: string): Record<string, string> {
+  const line = output.split('\n').find((l) => l.startsWith('IDS:'))
+  if (!line) throw new Error(`arranger printed no IDS line:\n${output}`)
+  return JSON.parse(line.slice('IDS:'.length))
+}
+
+/** SIGKILL the whole group and wait for the grandchild's death to settle. */
+async function sigkill(child: ReturnType<typeof spawn>): Promise<void> {
+  process.kill(-(child.pid as number), 'SIGKILL')
+  await new Promise<void>((r) => child.on('exit', () => r()))
+  await new Promise<void>((r) => setTimeout(r, 500))
+}
+
+/** The preamble every arranger child shares. */
+function childPreamble(root: string): string {
+  return `
+    import { Brainy } from ${JSON.stringify(join(REPO_ROOT, 'src', 'brainy.ts'))}
+    const ROOT = ${JSON.stringify(root)}
+    const brain = new Brainy<any>({ requireSubtype: false, storage: { type: 'filesystem', path: ROOT } })
+    const block = () => { (brain as any).kickEmbedWorker = () => {} }
+    const settleCheckpoint = async () => {
+      // The cadence write is fire-and-forget; wait for the single flight.
+      for (let i = 0; i < 200; i++) {
+        if (!(brain as any)._pendingEmbedCheckpointFlight) break
+        await (brain as any)._pendingEmbedCheckpointFlight.catch(() => {})
+      }
+    }
+  `
+}
+
+afterEach(async () => {
+  for (const brain of liveBrains.splice(0)) {
+    try { await brain.close() } catch { /* already closed / crashed — teardown only */ }
+  }
+  for (const d of roots.splice(0)) rmSync(d, { recursive: true, force: true })
+})
+
+// ===========================================================================
+// 1. The stuck-id brain — the defect, and the bound that now engages on it
+// ===========================================================================
+
+describe('pending-embed checkpoint — a brain whose pending set never drains', () => {
+  it('a permanently-stuck pending id: the reopen scans only the facts after the checkpoint', async () => {
+    const root = dir()
+    const first = await open(root, { blockWorker: true })
+    // add() returns the CANONICAL id (supplied ids are normalised), and that is
+    // the id the markers, the checkpoint and the fold all speak.
+    const stuck = await first.add({
+      id: 'stuck',
+      data: 'a deferred row whose embed never lands',
+      type: NounType.Thing,
+      deferEmbedding: true
+    })
+    expect(first.pendingEmbedCount()).toBe(1)
+    // Ordinary traffic after it — every one of these is a fact the unbounded
+    // fold had to re-read at every open, forever, because of that one id.
+    for (let i = 0; i < 12; i++) {
+      await first.add({ id: `row-${i}`, data: `row ${i}`, type: NounType.Thing })
+    }
+    await first.close()
+    liveBrains.splice(liveBrains.indexOf(first), 1)
+
+    // THE DEFECT, PINNED: the pending set never drained, so the old bound was
+    // never written — nothing on this brain could have shortened its fold.
+    expect(readArtifact(root, LOWWATER_PATH)).toBeNull()
+    // The checkpoint IS written at the clean close, set non-empty and all.
+    const checkpoint = readArtifact(root, CHECKPOINT_PATH) as {
+      generation: number
+      pending: string[]
+    } | null
+    expect(checkpoint).not.toBeNull()
+    expect(checkpoint!.generation).toBeGreaterThan(0)
+    expect(checkpoint!.pending).toEqual([stuck])
+
+    const second = await open(root, { blockWorker: true })
+    const report = foldReport(second)
+    // THE FIX, from the fold's own counter — not the clock.
+    expect(report.bound).toBe('checkpoint')
+    expect(report.fromGeneration).toBe(checkpoint!.generation + 1)
+    expect(report.factsScanned).toBe(0)
+    expect(report.seeded).toBe(1)
+    // The crash-recovery contract is intact: the marker is re-armed by open().
+    expect(pendingIds(second)).toEqual([stuck])
+    expect(second.pendingEmbedCount()).toBe(1)
+
+    // The differential: the bounded answer is the full-fold answer, and the
+    // full fold is what the previous bound would have had to read.
+    const full = await fullFold(second)
+    expect(full.ids).toEqual([stuck])
+    expect(full.facts).toBeGreaterThanOrEqual(13)
+    expect(report.factsScanned).toBeLessThan(full.facts)
+  }, 180_000)
+
+  it('the bound stays O(delta) across repeated opens while the id is still stuck', async () => {
+    const root = dir()
+    const first = await open(root, { blockWorker: true })
+    const stuck = await first.add({
+      id: 'stuck',
+      data: 'never lands',
+      type: NounType.Thing,
+      deferEmbedding: true
+    })
+    for (let i = 0; i < 6; i++) {
+      await first.add({ id: `a-${i}`, data: `a ${i}`, type: NounType.Thing })
+    }
+    await first.close()
+    liveBrains.splice(liveBrains.indexOf(first), 1)
+
+    const second = await open(root, { blockWorker: true })
+    expect(foldReport(second).factsScanned).toBe(0)
+    // More history under the same stuck id.
+    for (let i = 0; i < 9; i++) {
+      await second.add({ id: `b-${i}`, data: `b ${i}`, type: NounType.Thing })
+    }
+    await second.close()
+    liveBrains.splice(liveBrains.indexOf(second), 1)
+
+    const third = await open(root, { blockWorker: true })
+    const report = foldReport(third)
+    const full = await fullFold(third)
+    expect(report.bound).toBe('checkpoint')
+    expect(report.factsScanned).toBe(0)
+    // The unbounded fold grew with the store; the bounded one did not.
+    expect(full.facts).toBeGreaterThanOrEqual(16)
+    expect(pendingIds(third)).toEqual([stuck])
+    expect(full.ids).toEqual([stuck])
+  }, 180_000)
+})
+
+// ===========================================================================
+// 2. Torn checkpoint — falls back, loudly, correctly
+// ===========================================================================
+
+describe('pending-embed checkpoint — a torn checkpoint never shortens the fold', () => {
+  it('an undecodable checkpoint file degrades to the next bound, loudly, with the right pending set', async () => {
+    const root = dir()
+    const first = await open(root, { blockWorker: true })
+    const stuck = await first.add({
+      id: 'stuck',
+      data: 'never lands',
+      type: NounType.Thing,
+      deferEmbedding: true
+    })
+    for (let i = 0; i < 5; i++) {
+      await first.add({ id: `row-${i}`, data: `row ${i}`, type: NounType.Thing })
+    }
+    await first.close()
+    liveBrains.splice(liveBrains.indexOf(first), 1)
+
+    const onDisk = artifactPath(root, CHECKPOINT_PATH)
+    expect(onDisk).not.toBeNull()
+    // Tear it: bytes that are neither valid gzip nor valid JSON. A torn file
+    // must THROW on read — never parse into a partial `pending` list.
+    writeFileSync(onDisk!, 'not a checkpoint at all {{{')
+
+    const before = getTornRecordGauge().count
+    const { result: second, lines } = await captureConsole(async () =>
+      open(root, { blockWorker: true })
+    )
+    const report = foldReport(second)
+    // Fell back — never to a shorter bound, and never silently.
+    expect(report.bound).not.toBe('checkpoint')
+    expect(report.seeded).toBe(0)
+    expect(report.fromGeneration).toBe(1) // no mark either: this brain never drained
+    // LOUD, two ways: the adapter's torn-record gauge and its production error…
+    expect(getTornRecordGauge().count).toBeGreaterThan(before)
+    expect(getTornRecordGauge().lastPath).toContain('pending_embeds_checkpoint')
+    expect(lines.some((l) => /TORN RECORD/.test(l))).toBe(true)
+    // …and the fold's own narration of which bound it actually used.
+    expect(lines.some((l) => /pending-embed fold: genesis bound/.test(l))).toBe(true)
+
+    // CORRECT: the marker is still recovered, from the log itself.
+    expect(pendingIds(second)).toEqual([stuck])
+    const full = await fullFold(second)
+    expect(full.ids).toEqual([stuck])
+    expect(report.factsScanned).toBe(full.facts)
+  }, 180_000)
+
+  it('a well-formed but shape-invalid checkpoint is refused whole, never partially trusted', async () => {
+    const root = dir()
+    const first = await open(root, { blockWorker: true })
+    const stuck = await first.add({
+      id: 'stuck',
+      data: 'never lands',
+      type: NounType.Thing,
+      deferEmbedding: true
+    })
+    await first.add({ id: 'other', data: 'ordinary row', type: NounType.Thing })
+    await first.close()
+    liveBrains.splice(liveBrains.indexOf(first), 1)
+
+    // A checkpoint with a plausible generation but a `pending` that is not a
+    // list of ids: trusting the generation alone would bound the scan behind a
+    // set that was never recovered — the exact shape that loses a vector.
+    const onDisk = artifactPath(root, CHECKPOINT_PATH)!
+    const good = readArtifact(root, CHECKPOINT_PATH) as { generation: number }
+    rmSync(onDisk)
+    writeFileSync(
+      join(root, '_system', 'pending_embeds_checkpoint.json'),
+      JSON.stringify({ generation: good.generation, pending: { stuck: true }, writtenAt: 1 })
+    )
+
+    const { result: second, lines } = await captureConsole(async () =>
+      open(root, { blockWorker: true })
+    )
+    expect(lines.some((l) => /pending-embed checkpoint REFUSED/.test(l))).toBe(true)
+    const report = foldReport(second)
+    expect(report.bound).not.toBe('checkpoint')
+    expect(report.seeded).toBe(0)
+    expect(pendingIds(second)).toEqual([stuck])
+  }, 180_000)
+})
+
+// ===========================================================================
+// 3. The crash matrix — real processes, real SIGKILL, differential invariant
+// ===========================================================================
+
+describe('pending-embed checkpoint — crash matrix (real child process, SIGKILL)', () => {
+  /**
+   * The invariant every row shares: whatever the reopened brain's fold did with
+   * whatever bound survived the crash, its pending set must equal the truth a
+   * full fold from generation 1 derives from the SAME recovered log.
+   */
+  async function assertDifferentialAfterCrash(root: string): Promise<{
+    report: FoldReport
+    full: { ids: string[]; facts: number }
+    pending: string[]
+  }> {
+    const reopened = await open(root, { blockWorker: true })
+    const report = foldReport(reopened)
+    const full = await fullFold(reopened)
+    const pending = pendingIds(reopened)
+    expect(pending).toEqual(full.ids)
+    return { report, full, pending }
+  }
+
+  it('killed BEFORE any checkpoint was written — falls back and recovers the marker from the log', async () => {
+    const root = dir()
+    const { child, output } = await spawnArranger(
+      root,
+      `${childPreamble(root)}
+      block()
+      await brain.init()
+      await brain.add({ id: 'landed-row', data: 'an ordinary row', type: 'thing' })
+      const stuck = await brain.add({ id: 'stuck-1', data: 'deferred, never lands', type: 'thing', deferEmbedding: true })
+      await brain.flush()
+      console.log('IDS:' + JSON.stringify({ stuck }))
+      console.log('READY')
+      setInterval(() => {}, 1000)
+      `
+    )
+    const ids = childIds(output())
+    // One enqueue is well under the cadence and the set never drained, so no
+    // checkpoint exists — this is the pre-checkpoint crash.
+    expect(readArtifact(root, CHECKPOINT_PATH)).toBeNull()
+    await sigkill(child)
+
+    const { report, pending } = await assertDifferentialAfterCrash(root)
+    expect(report.bound).toBe('genesis')
+    expect(pending).toEqual([ids.stuck])
+  }, 300_000)
+
+  it('killed AFTER a checkpoint, with an embed landed and flushed after it — the post-checkpoint facts carry the disarm', async () => {
+    const root = dir()
+    const { child, output } = await spawnArranger(
+      root,
+      `${childPreamble(root)}
+      await brain.init()
+      // Land one deferred embed: the drain arms the checkpoint debt.
+      await brain.add({ id: 'seed', data: 'lands first', type: 'thing', deferEmbedding: true })
+      await brain.awaitPendingEmbeds()
+      await brain.flush()
+      // A second deferred write pays the debt (the head is at the manifest now),
+      // then LANDS — its embed.landed rides a fact ABOVE the checkpoint.
+      const landsAfter = await brain.add({ id: 'lands-after', data: 'lands after the checkpoint', type: 'thing', deferEmbedding: true })
+      await settleCheckpoint()
+      await brain.awaitPendingEmbeds()
+      // …and one that never will.
+      block()
+      const stuck = await brain.add({ id: 'stuck-1', data: 'deferred, never lands', type: 'thing', deferEmbedding: true })
+      await brain.add({ id: 'plain', data: 'more history', type: 'thing' })
+      await brain.flush()
+      console.log('IDS:' + JSON.stringify({ stuck, landsAfter }))
+      console.log('READY')
+      setInterval(() => {}, 1000)
+      `
+    )
+    const ids = childIds(output())
+    const checkpoint = readArtifact(root, CHECKPOINT_PATH) as {
+      generation: number
+      pending: string[]
+    } | null
+    expect(checkpoint).not.toBeNull()
+    await sigkill(child)
+
+    const { report, full, pending } = await assertDifferentialAfterCrash(root)
+    expect(report.bound).toBe('checkpoint')
+    expect(report.fromGeneration).toBe(checkpoint!.generation + 1)
+    // The bound really bounded: fewer facts than the whole log.
+    expect(report.factsScanned).toBeLessThan(full.facts)
+    // A landed embed above the checkpoint is disarmed by the scan, not lost;
+    // the stuck one is re-armed.
+    expect(pending).toEqual([ids.stuck])
+    expect(pending).not.toContain(ids.landsAfter)
+  }, 300_000)
+
+  it('killed AFTER a checkpoint with an UN-FLUSHED tail — truncated facts and the bounded fold still agree', async () => {
+    const root = dir()
+    const { child } = await spawnArranger(
+      root,
+      `${childPreamble(root)}
+      await brain.init()
+      await brain.add({ id: 'seed', data: 'lands first', type: 'thing', deferEmbedding: true })
+      await brain.awaitPendingEmbeds()
+      await brain.flush()
+      await brain.add({ id: 'lands-after', data: 'lands after the checkpoint', type: 'thing', deferEmbedding: true })
+      await settleCheckpoint()
+      await brain.awaitPendingEmbeds()
+      await brain.flush()
+      // Now write PAST the manifest and never flush: these facts are the tail a
+      // crash truncates. Whatever survives, the two folds must agree on it.
+      block()
+      await brain.add({ id: 'stuck-tail', data: 'deferred, never lands', type: 'thing', deferEmbedding: true })
+      await brain.add({ id: 'plain-tail', data: 'unflushed history', type: 'thing' })
+      console.log('READY')
+      setInterval(() => {}, 1000)
+      `
+    )
+    const checkpoint = readArtifact(root, CHECKPOINT_PATH) as { generation: number } | null
+    expect(checkpoint).not.toBeNull()
+    await sigkill(child)
+
+    const { report } = await assertDifferentialAfterCrash(root)
+    // The checkpoint's generation is at or below the manifest by construction,
+    // so it survived the truncation and still bounds the fold.
+    expect(report.bound).toBe('checkpoint')
+    expect(report.fromGeneration).toBe(checkpoint!.generation + 1)
+  }, 300_000)
+})

tests/integration/pending-embed-low-water.test.ts

@@ -0,0 +1,141 @@
+/**
+ * @module tests/integration/pending-embed-low-water
+ * @description The pending-embed recovery fold is bounded and background (10.4.9).
+ *
+ * The fold used to scan the generation log from generation 1 at EVERY open,
+ * on the open's foreground — O(whole history) per open on long-lived brains.
+ * Now: an advisory low-water mark (`_system/pending_embeds_lowwater.json`)
+ * records the committed generation whenever the pending set drains to empty,
+ * recovery scans from `mark + 1` on the open's foreground — the crash-recovery
+ * contract keeps markers re-armed when open() returns. The mark is advisory: stale-low costs a longer scan, never a
+ * marker — a pending embed enqueued before a crash is still recovered.
+ */
+import { describe, it, expect, afterEach, vi } from 'vitest'
+import { mkdtempSync, rmSync } from 'node:fs'
+import { tmpdir } from 'node:os'
+import { join } from 'node:path'
+import { Brainy } from '../../src/brainy'
+import { NounType } from '../../src/types/graphTypes'
+
+const LOWWATER_PATH = '_system/pending_embeds_lowwater.json'
+
+describe('pending-embed recovery: bounded by the low-water mark', () => {
+  const roots: string[] = []
+  const dir = (): string => {
+    const d = mkdtempSync(join(tmpdir(), 'brainy-lowwater-'))
+    roots.push(d)
+    return d
+  }
+  const open = async (root: string): Promise<Brainy<any>> => {
+    const brain = new Brainy<any>({
+      requireSubtype: false,
+      storage: { type: 'filesystem', path: root }
+    })
+    await brain.init()
+    return brain
+  }
+
+  afterEach(() => {
+    for (const d of roots.splice(0)) rmSync(d, { recursive: true, force: true })
+  })
+
+  it('drain-to-empty writes the mark, and the next open scans from mark + 1', async () => {
+    const root = dir()
+    const brain = await open(root)
+    // Hold the worker so the pending state is observable, then release it.
+    const realKick = (brain as any).kickEmbedWorker.bind(brain)
+    ;(brain as any).kickEmbedWorker = () => {}
+    await brain.add({
+      id: 'row-1',
+      data: 'the first deferred row',
+      type: NounType.Thing,
+      deferEmbedding: true
+    })
+    expect(brain.pendingEmbedCount()).toBeGreaterThan(0)
+    ;(brain as any).kickEmbedWorker = realKick
+    await brain.awaitPendingEmbeds()
+    // The drain wrote the advisory mark (fire-and-forget: settle the microtask).
+    await new Promise((r) => setTimeout(r, 50))
+    const mark = (await (brain as any).storage.readRawObject(LOWWATER_PATH)) as {
+      generation: number
+    } | null
+    expect(mark).not.toBeNull()
+    expect(mark!.generation).toBeGreaterThan(0)
+    await brain.close()
+
+    const brain2 = await open(root)
+    const log = (brain2 as any).generationStore.getFactLog()
+    const scanSpy = vi.spyOn(log, 'scanFacts')
+    try {
+      await (brain2 as any).recoverPendingEmbedsFromLog()
+      expect(scanSpy).toHaveBeenCalledTimes(1)
+      const opts = scanSpy.mock.calls[0][0] as { fromGeneration?: number }
+      expect(opts.fromGeneration).toBeGreaterThanOrEqual(mark!.generation + 1)
+    } finally {
+      scanSpy.mockRestore()
+      await brain2.close()
+    }
+  })
+
+  it('a pending embed enqueued after the mark survives an unclean stop', async () => {
+    const root = dir()
+    const brain = await open(root)
+    await brain.add({ id: 'settled', data: 'lands before the mark', type: NounType.Thing })
+    await brain.awaitPendingEmbeds()
+    await new Promise((r) => setTimeout(r, 50))
+
+    // A deferred write whose embed never lands: block the worker, then drop
+    // the instance without close() — the unclean-stop shape.
+    ;(brain as any).kickEmbedWorker = () => {}
+    await brain.add({
+      id: 'orphan',
+      data: 'enqueued then abandoned',
+      type: NounType.Thing,
+      deferEmbedding: true
+    })
+    expect(brain.pendingEmbedCount()).toBeGreaterThan(0)
+    // No close(): simulate the crash by releasing only the writer lock so the
+    // next open can proceed.
+    await (brain as any).storage.releaseWriterLock()
+
+    const brain2 = await open(root)
+    expect(brain2.pendingEmbedCount()).toBeGreaterThan(0)
+    await brain2.awaitPendingEmbeds()
+    expect(brain2.pendingEmbedCount()).toBe(0)
+    await brain2.close()
+    // Reap the crashed instance: its fence is gone, so close() fails loudly —
+    // swallow that here; the point is clearing its watchers and registry entry.
+    await brain.close().catch(() => undefined)
+  })
+
+  it('a reopened brain has its pending set settled when open() returns', async () => {
+    const root = dir()
+    const brain = await open(root)
+    await brain.add({ id: 'a-row', data: 'some data', type: NounType.Thing })
+    await brain.awaitPendingEmbeds()
+    await brain.close()
+
+    const brain2 = await open(root)
+    // The crash-recovery contract: markers are re-armed by open itself —
+    // no latch, no background race. (Here the drain landed, so zero.)
+    expect(brain2.pendingEmbedCount()).toBe(0)
+    await brain2.close()
+  })
+
+  it('a clean close with an empty set writes the mark even if no drain happened', async () => {
+    const root = dir()
+    const brain = await open(root)
+    await brain.add({ id: 'r1', data: 'row one', type: NounType.Thing })
+    await brain.awaitPendingEmbeds()
+    await brain.close()
+    // Read the mark back through the storage door (the adapter owns the
+    // on-disk encoding), on a fresh instance.
+    const brain2 = await open(root)
+    const mark = (await (brain2 as any).storage.readRawObject(LOWWATER_PATH)) as {
+      generation: number
+    } | null
+    expect(mark).not.toBeNull()
+    expect(mark!.generation).toBeGreaterThan(0)
+    await brain2.close()
+  })
+})

tests/integration/readonly-close-no-marker.test.ts

@@ -0,0 +1,250 @@
+/**
+ * @module tests/integration/readonly-close-no-marker
+ * @description A READ-ONLY BRAIN WRITES NO CLEAN-SHUTDOWN EVIDENCE.
+ *
+ * `_system/clean-shutdown.json` is the WRITER's own word about the writer's
+ * own process: "everything above this line, from THIS session, is durable."
+ * Two call sites treated a reader exactly like a writer:
+ *
+ *   1. `Brainy#closeDurableSteps()` called `generationStore.close()`
+ *      unconditionally — a reader's close re-stamped the marker at the
+ *      generation the reader merely OBSERVED, never committed.
+ *   2. `GenerationStore#open()` consumed (deleted) the marker on every open,
+ *      reader or writer alike, so a reader that never got to a matching
+ *      close left the store looking crashed to the next writer.
+ *
+ * Both are fixed by making a read-only brain leave `_system/` exactly as it
+ * found it — at open AND at close. Pinned here:
+ *
+ *   1. `_system/` is byte-for-byte identical (file set + contents) before and
+ *      after a reader opens a cleanly-closed store, reads it, and closes.
+ *   2. After the reader's close, the next WRITER open adopts the marker as
+ *      clean — no recovery fold narrates.
+ *   3. A reader creates no file under `_system/` merely by opening (before it
+ *      ever closes).
+ *   4. A reader that opens and is then abandoned (crash-style, no close) does
+ *      not force the next writer to pay a recovery fold — the concrete harm
+ *      the fix closes.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest'
+import { mkdtempSync, rmSync, readdirSync, readFileSync, statSync } from 'node:fs'
+import { createHash } from 'node:crypto'
+import { tmpdir } from 'node:os'
+import { join } from 'node:path'
+import { Brainy } from '../../src/brainy.js'
+import { NounType } from '../../src/types/graphTypes.js'
+import { abandonAsCrashed } from '../helpers/durabilityKillMatrix.js'
+
+function makeTempDir(): string {
+  return mkdtempSync(join(tmpdir(), 'brainy-readonly-close-'))
+}
+
+/** Recursively hash every regular file under `dir`, keyed by its path relative to `dir`. */
+function snapshotDir(dir: string): Map<string, string> {
+  const out = new Map<string, string>()
+  const walk = (rel: string): void => {
+    const abs = rel ? join(dir, rel) : dir
+    let entries: string[]
+    try {
+      entries = readdirSync(abs)
+    } catch {
+      return
+    }
+    for (const name of entries) {
+      const childRel = rel ? join(rel, name) : name
+      const childAbs = join(dir, childRel)
+      const st = statSync(childAbs)
+      if (st.isDirectory()) {
+        walk(childRel)
+      } else if (st.isFile()) {
+        const hash = createHash('sha256').update(readFileSync(childAbs)).digest('hex')
+        out.set(childRel, hash)
+      }
+    }
+  }
+  walk('')
+  return out
+}
+
+/** Capture console.warn lines (the narration channel — see `prodLog.narrate`) while `fn` runs. */
+async function captureWarn<T>(fn: () => Promise<T>): Promise<{ result: T; lines: string[] }> {
+  const lines: string[] = []
+  const orig = console.warn
+  console.warn = ((...args: unknown[]) => {
+    lines.push(args.map((a) => String(a)).join(' '))
+  }) as typeof console.warn
+  try {
+    return { result: await fn(), lines }
+  } finally {
+    console.warn = orig
+  }
+}
+
+describe('a read-only brain writes no clean-shutdown evidence', () => {
+  let dir: string
+  let brain: Brainy | null = null
+
+  beforeEach(() => {
+    dir = makeTempDir()
+  })
+
+  afterEach(async () => {
+    if (brain) {
+      try {
+        await brain.close()
+      } catch {
+        /* already closed */
+      }
+      brain = null
+    }
+    try {
+      rmSync(dir, { recursive: true, force: true })
+    } catch {
+      /* ignore */
+    }
+  })
+
+  const systemDir = () => join(dir, '_system')
+  /**
+   * The marker file's actual on-disk name — `clean-shutdown.json` or, under
+   * FileSystemStorage's default gzip compression, `clean-shutdown.json.gz`.
+   * Returns null when absent.
+   */
+  const findMarkerPath = (): string | null => {
+    let entries: string[]
+    try {
+      entries = readdirSync(systemDir())
+    } catch {
+      return null
+    }
+    const name = entries.find((n) => n.startsWith('clean-shutdown.json'))
+    return name ? join(systemDir(), name) : null
+  }
+
+  it('leaves `_system/`\'s file set and the clean-shutdown marker\'s bytes identical across a reader open → read → close', async () => {
+    // A writer opens, writes, and closes cleanly — the marker lands at
+    // whatever generation the writer actually committed.
+    const writer = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dir } })
+    await writer.init()
+    await writer.add({ data: 'seed entity', type: NounType.Concept })
+    await writer.add({ data: 'second entity', type: NounType.Concept })
+    await writer.flush()
+    await writer.close()
+
+    const markerBeforePath = findMarkerPath()
+    expect(markerBeforePath, 'the writer left a clean-shutdown marker').not.toBeNull()
+    const before = snapshotDir(systemDir())
+    expect(before.size).toBeGreaterThan(0)
+    const markerBeforeHash = before.get(
+      (markerBeforePath as string).slice(systemDir().length + 1)
+    )
+    expect(markerBeforeHash).toBeTruthy()
+
+    // A reader opens the same store, reads, and closes.
+    brain = await Brainy.openReadOnly({ storage: { type: 'filesystem', path: dir } })
+    expect(brain.isReadOnly).toBe(true)
+    await brain.stats()
+    await brain.close()
+    brain = null
+
+    // The FILE SET under `_system/` is unchanged — a reader creates and
+    // removes nothing. (Other files under `_system/` — e.g. the metadata
+    // field registry, which stamps its own `lastUpdated` on every persist —
+    // are a pre-existing, separate concern outside this fix's scope: this
+    // pin is specifically about the generation store's clean-shutdown
+    // evidence, not about every subsystem's close() being a true no-op for
+    // a reader.)
+    const after = snapshotDir(systemDir())
+    expect([...after.keys()].sort()).toEqual([...before.keys()].sort())
+
+    // The MARKER's bytes are byte-for-byte identical — the reader neither
+    // consumed it at open nor re-stamped it at close.
+    const markerAfterPath = findMarkerPath()
+    expect(markerAfterPath, 'the marker must still exist, under the same name').toBe(markerBeforePath)
+    const markerAfterHash = after.get((markerAfterPath as string).slice(systemDir().length + 1))
+    expect(markerAfterHash).toBe(markerBeforeHash)
+  }, 120_000)
+
+  it('creates no file under `_system/` merely by opening read-only', async () => {
+    const writer = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dir } })
+    await writer.init()
+    await writer.add({ data: 'seed entity', type: NounType.Concept })
+    await writer.flush()
+    await writer.close()
+
+    const baselineNames = [...snapshotDir(systemDir()).keys()].sort()
+    expect(baselineNames.length).toBeGreaterThan(0)
+
+    // Open the reader and inspect `_system/` BEFORE it ever closes — open()
+    // alone must create nothing.
+    brain = await Brainy.openReadOnly({ storage: { type: 'filesystem', path: dir } })
+    const whileOpenNames = [...snapshotDir(systemDir()).keys()].sort()
+    expect(whileOpenNames).toEqual(baselineNames)
+
+    await brain.close()
+    brain = null
+  }, 120_000)
+
+  it('a writer reopening after the reader closes adopts the marker — no recovery fold', async () => {
+    const writer1 = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dir } })
+    await writer1.init()
+    await writer1.add({ data: 'seed entity', type: NounType.Concept })
+    await writer1.flush()
+    await writer1.close()
+
+    // A reader opens and closes in between — must not disturb the marker.
+    const reader = await Brainy.openReadOnly({ storage: { type: 'filesystem', path: dir } })
+    await reader.stats()
+    await reader.close()
+
+    // The next writer open must be a clean, no-fold open: no
+    // "log-authority recovery" / "WHOLE-LOG fold" narration line.
+    const { result: writer2, lines } = await captureWarn(async () => {
+      const w = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dir } })
+      await w.init()
+      return w
+    })
+    brain = writer2
+
+    const foldLines = lines.filter((l) => /log-authority recovery|WHOLE-LOG fold|recovery fold/i.test(l))
+    expect(foldLines, `unexpected recovery narration:\n${foldLines.join('\n')}`).toEqual([])
+
+    // And the store is exactly what the first writer left — the seed row is
+    // still there, nothing was rolled back or re-derived.
+    const found = await writer2.find({ where: {} } as any)
+    expect(found.length).toBeGreaterThanOrEqual(1)
+  }, 120_000)
+
+  it('a reader that opens and is then abandoned (never closes) does not force the next writer to fold', async () => {
+    // This is the concrete harm the fix closes: pre-fix, a reader's open()
+    // unconditionally DELETED the marker (consuming it as if it were the
+    // writer). A reader that opened and then died — no close, exactly like
+    // a killed process — left the marker gone, so the actual writer's next
+    // open read the store as crashed and paid a full recovery fold for a
+    // "crash" that was really just a reader that came and went.
+    const writer1 = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dir } })
+    await writer1.init()
+    await writer1.add({ data: 'seed entity', type: NounType.Concept })
+    await writer1.flush()
+    await writer1.close()
+
+    const reader = await Brainy.openReadOnly({ storage: { type: 'filesystem', path: dir } })
+    await reader.stats()
+    // NEVER calls reader.close() — abandon it exactly like a killed process.
+    await abandonAsCrashed(reader)
+
+    const { result: writer2, lines } = await captureWarn(async () => {
+      const w = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dir } })
+      await w.init()
+      return w
+    })
+    brain = writer2
+
+    const foldLines = lines.filter((l) => /log-authority recovery|WHOLE-LOG fold|recovery fold/i.test(l))
+    expect(
+      foldLines,
+      `an abandoned READER forced a recovery fold on the next writer open:\n${foldLines.join('\n')}`
+    ).toEqual([])
+  }, 120_000)
+})

tests/integration/related-verb-array.test.ts

@@ -0,0 +1,89 @@
+/**
+ * @module tests/integration/related-verb-array
+ * @description related() honours EVERY verb type in an array (10.4.9).
+ *
+ * The storage fast paths for `sourceId + verbType` and `verbType` collapsed a
+ * verb-type ARRAY to its first element — `related({ from, type: [a, b] })`
+ * silently returned only `a` edges, whichever order the array came in. The
+ * same quiet-loss class as the graph-first paging defect, one seam over.
+ * These pins seed a store where the SECOND requested type's edge must come
+ * back, on every path the collapse lived in.
+ */
+import { describe, it, expect, beforeAll, afterAll } from 'vitest'
+import { Brainy } from '../../src/brainy'
+import { NounType, VerbType } from '../../src/types/graphTypes'
+import { v5 } from '../../src/universal/uuid'
+
+describe('related() with a verb-type array returns every requested type', () => {
+  let brain: Brainy<any>
+
+  beforeAll(async () => {
+    brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+    for (const id of ['a', 'b', 'c', 'd']) {
+      await brain.add({ id, data: `node ${id}`, type: NounType.Person })
+    }
+    await brain.relate({ from: 'a', to: 'b', type: VerbType.Supports })
+    await brain.relate({ from: 'a', to: 'c', type: VerbType.RelatedTo })
+    await brain.relate({ from: 'a', to: 'd', type: VerbType.Knows })
+    await brain.relate({ from: 'b', to: 'c', type: VerbType.RelatedTo })
+  })
+
+  afterAll(async () => {
+    brain = null as any
+  })
+
+  it('from + type array: the second type\'s edge comes back, both orders', async () => {
+    for (const types of [
+      [VerbType.Supports, VerbType.RelatedTo],
+      [VerbType.RelatedTo, VerbType.Supports]
+    ]) {
+      const edges = await brain.related({ from: 'a', type: types })
+      const targets = new Set(edges.map((e) => e.to))
+      expect(targets.has(v5('b')), `types [${types}] missing Supports edge`).toBe(true)
+      expect(targets.has(v5('c')), `types [${types}] missing RelatedTo edge`).toBe(true)
+      expect(targets.has(v5('d'))).toBe(false)
+      expect(edges).toHaveLength(2)
+    }
+  })
+
+  it('a single-element array behaves exactly like the scalar', async () => {
+    const scalar = await brain.related({ from: 'a', type: VerbType.Supports })
+    const array = await brain.related({ from: 'a', type: [VerbType.Supports] })
+    expect(array.map((e) => e.id).sort()).toEqual(scalar.map((e) => e.id).sort())
+    expect(array).toHaveLength(1)
+  })
+
+  it('no duplicate edges when types overlap the same edge set', async () => {
+    const edges = await brain.related({
+      from: 'a',
+      type: [VerbType.Supports, VerbType.RelatedTo, VerbType.Knows]
+    })
+    const ids = edges.map((e) => e.id)
+    expect(new Set(ids).size).toBe(ids.length)
+    expect(edges).toHaveLength(3)
+  })
+
+  it('type-only asks (no anchor) honour the whole array too', async () => {
+    const edges = await brain.related({ type: [VerbType.Supports, VerbType.Knows] })
+    const verbs = new Set(edges.map((e) => e.type))
+    expect(verbs.has(VerbType.Supports)).toBe(true)
+    expect(verbs.has(VerbType.Knows)).toBe(true)
+    expect(edges).toHaveLength(2)
+  })
+
+  it('to + type array: the target side honours every type too', async () => {
+    const edges = await brain.related({ to: 'c', type: [VerbType.RelatedTo, VerbType.Supports] })
+    const froms = new Set(edges.map((e) => e.from))
+    expect(froms.has(v5('a'))).toBe(true)
+    expect(froms.has(v5('b'))).toBe(true)
+    expect(edges).toHaveLength(2)
+  })
+
+  it('pagination stays consistent across the union', async () => {
+    const page1 = await brain.related({ from: 'a', type: [VerbType.Supports, VerbType.RelatedTo, VerbType.Knows], limit: 2 })
+    const page2 = await brain.related({ from: 'a', type: [VerbType.Supports, VerbType.RelatedTo, VerbType.Knows], limit: 2, offset: 2 })
+    const all = [...page1, ...page2].map((e) => e.id)
+    expect(new Set(all).size).toBe(3)
+  })
+})

tests/integration/shutdown-single-owner.test.ts

@@ -0,0 +1,405 @@
+/**
+ * @module tests/integration/shutdown-single-owner
+ * @description ONE SHUTDOWN, ONE OWNER.
+ *
+ * MEASURED IN PRODUCTION. A host that owns its own shutdown — one SIGTERM
+ * listener calling `close()` on every pooled store — ran head-on into the
+ * engine's own signal handler, which iterated every live instance, flushed its
+ * components in parallel, and released its writer lock in a `finally`. Two
+ * teardowns of the same brain at the same moment. The log shape:
+ *
+ *   "Shutdown signal received - flushing pending data..."   (SIGTERM)
+ *   ...148 seconds of silence...
+ *   "Flushed successfully (1 instance)"
+ *   ...the host's pool close of that same store returns 1s later
+ *
+ * 149s for the one store with engine work in flight, against 24s for its six
+ * idle siblings. The same race in a local reproduction printed
+ * `Failed to flush one Brainy instance on shutdown: Writer fence lost … the
+ * lock file is gone` — the handler observing a lock the close it was racing
+ * had already released.
+ *
+ * The contract pinned here:
+ *   (a) A host owner and the engine's hooks both live: EXACTLY ONE close runs
+ *       per brain, no fence is lost, both durability markers are written, the
+ *       process exits 0, and the reopen adopts rather than folding.
+ *   (b) No host owner: the engine's handler closes every instance by the same
+ *       `close()` path — markers written, clean exit.
+ *   (c) `close()` is idempotent and re-entrant: concurrent callers share ONE
+ *       execution and all of them settle.
+ *   (d) Flush is single-flight: N kicks during a running flush arm exactly one
+ *       follow-up, and two flush bodies never overlap.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest'
+import { mkdtempSync, rmSync, existsSync, readFileSync, writeFileSync } from 'node:fs'
+import { spawn } from 'node:child_process'
+import { tmpdir } from 'node:os'
+import { join } from 'node:path'
+import { Brainy } from '../../src/brainy.js'
+import { NounType } from '../../src/types/graphTypes.js'
+
+const REPO_ROOT = process.cwd()
+const TSX = join(REPO_ROOT, 'node_modules', '.bin', 'tsx')
+const BRAINY_SRC = join(REPO_ROOT, 'src', 'brainy.ts')
+
+function makeTempDir(prefix: string): string {
+  return mkdtempSync(join(tmpdir(), prefix))
+}
+
+/** The writer lock's clean-close record — written by `releaseWriterLock()`. */
+const closeRecordPath = (dir: string) => join(dir, 'locks', '_writer.close')
+/**
+ * The generation store's clean-shutdown marker — the adopt-vs-fold gate.
+ * (`FileSystemStorage` gzips raw objects, so the file on disk carries `.gz`;
+ * both spellings are accepted so the pin survives a compression change.)
+ */
+const cleanShutdownWritten = (dir: string) =>
+  existsSync(join(dir, '_system', 'clean-shutdown.json.gz')) ||
+  existsSync(join(dir, '_system', 'clean-shutdown.json'))
+
+/**
+ * Write a child script and start it under tsx, in its OWN process group so a
+ * group-wide signal reaches the grandchild that actually holds the writer
+ * lock. (A file, not `tsx -e`: the eval form compiles to CommonJS, which has
+ * no top-level await.)
+ */
+function startChild(scriptDir: string, body: string): ReturnType<typeof spawn> {
+  const scriptPath = join(scriptDir, 'child-process.mts')
+  writeFileSync(scriptPath, body)
+  return spawn(TSX, [scriptPath], {
+    cwd: REPO_ROOT,
+    stdio: ['ignore', 'pipe', 'pipe'],
+    detached: true
+  })
+}
+
+/** Start a child and resolve once it prints READY, collecting all its output. */
+function startAndAwaitReady(
+  scriptDir: string,
+  body: string
+): Promise<{ child: ReturnType<typeof spawn>; output: () => string }> {
+  const child = startChild(scriptDir, body)
+  let out = ''
+  child.stdout?.on('data', (d) => { out += String(d) })
+  child.stderr?.on('data', (d) => { out += String(d) })
+  return new Promise((resolvePromise, rejectPromise) => {
+    const timer = setTimeout(
+      () => rejectPromise(new Error(`child never became READY:\n${out}`)),
+      120_000
+    )
+    child.stdout?.on('data', () => {
+      if (out.includes('READY')) {
+        clearTimeout(timer)
+        resolvePromise({ child, output: () => out })
+      }
+    })
+    child.on('exit', (code) => {
+      clearTimeout(timer)
+      if (!out.includes('READY')) rejectPromise(new Error(`child exited ${code} before READY:\n${out}`))
+    })
+  })
+}
+
+/** Capture console.warn/error/log lines emitted while `fn` runs. */
+async function captureConsole<T>(fn: () => Promise<T>): Promise<{ result: T; lines: string[] }> {
+  const lines: string[] = []
+  const orig = { log: console.log, warn: console.warn, error: console.error }
+  const sink = (...args: unknown[]) => { lines.push(args.map((a) => String(a)).join(' ')) }
+  console.log = sink as typeof console.log
+  console.warn = sink as typeof console.warn
+  console.error = sink as typeof console.error
+  try {
+    return { result: await fn(), lines }
+  } finally {
+    console.log = orig.log
+    console.warn = orig.warn
+    console.error = orig.error
+  }
+}
+
+/**
+ * Reopen a store and assert the open ADOPTED: no crash-recovery fold, no
+ * stale-lock verdict. This is the whole point of a close having run exactly
+ * once — a fold is measured in tens of seconds on a real store.
+ */
+async function expectCleanReopen(dir: string): Promise<void> {
+  const { result, lines } = await captureConsole(async () => {
+    const next = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dir } })
+    await next.init()
+    return next
+  })
+  try {
+    expect(lines.filter((l) => /log-authority recovery|unclean shutdown detected/i.test(l))).toEqual([])
+    expect(lines.filter((l) => /Overwriting stale writer lock|appears dead/i.test(l))).toEqual([])
+  } finally {
+    await result.close()
+  }
+}
+
+/** The child's counts of closes entered and close bodies run, per brain. */
+function readResult(
+  resultPath: string,
+  out: string
+): { entries: Record<string, number>; bodies: Record<string, number>; releases: Record<string, number> } {
+  if (!existsSync(resultPath)) throw new Error(`child wrote no result file:\n${out}`)
+  return JSON.parse(readFileSync(resultPath, 'utf-8'))
+}
+
+/**
+ * The child-side instrumentation, shared by (a) and (b): count how many times
+ * `close()` is ENTERED per brain and how many times its body actually RUNS.
+ * The counting wrapper is an OWN property, so it shadows the prototype for
+ * every caller — including the engine's own signal handler, which calls
+ * `instance.close()`.
+ *
+ * `report()` writes SYNCHRONOUSLY to a file: it runs on the way out of the
+ * process (the engine's handler calls `process.exit(0)` when it is the sole
+ * shutdown owner), and a `console.log` to a pipe is asynchronous and can be
+ * dropped by that exit.
+ */
+function childCounters(resultPath: string): string {
+  return `
+  const entries = {}
+  const bodies = {}
+  const releases = {}
+  function instrument(name, brain) {
+    entries[name] = 0
+    bodies[name] = 0
+    releases[name] = 0
+    const enter = brain.close.bind(brain)
+    brain.close = () => { entries[name]++; return enter() }
+    const durable = brain.closeDurableSteps.bind(brain)
+    brain.closeDurableSteps = () => { bodies[name]++; return durable() }
+    // The writer lock is the ownership witness: the old handler released it
+    // in its own finally, on top of the owner's close doing the same.
+    const storage = brain.storage
+    const release = storage.releaseWriterLock.bind(storage)
+    storage.releaseWriterLock = () => { releases[name]++; return release() }
+  }
+  const report = () => {
+    __writeFileSync(${JSON.stringify(resultPath)}, JSON.stringify({ entries, bodies, releases }))
+  }
+`
+}
+
+describe('shutdown has exactly one owner', () => {
+  let dirA: string
+  let dirB: string
+  let scriptDir: string
+  let resultPath: string
+
+  beforeEach(() => {
+    dirA = makeTempDir('brainy-shutdown-owner-a-')
+    dirB = makeTempDir('brainy-shutdown-owner-b-')
+    scriptDir = makeTempDir('brainy-shutdown-owner-script-')
+    resultPath = join(scriptDir, 'result.json')
+  })
+
+  afterEach(() => {
+    for (const d of [dirA, dirB, scriptDir]) {
+      try { rmSync(d, { recursive: true, force: true }) } catch { /* ignore */ }
+    }
+  })
+
+  it('(a) a host owner closes both brains and the engine handler steps aside', async () => {
+    const script = `
+      import { writeFileSync as __writeFileSync } from 'node:fs'
+      import { Brainy } from ${JSON.stringify(BRAINY_SRC)}
+      const a = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: ${JSON.stringify(dirA)} } })
+      const b = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: ${JSON.stringify(dirB)} } })
+      await a.init()
+      await b.init()
+      await a.add({ data: 'row in brain a', type: 'concept' })
+      await b.add({ data: 'row in brain b', type: 'concept' })
+      ${childCounters(resultPath)}
+      instrument('a', a)
+      instrument('b', b)
+      // THE HOST'S OWN SHUTDOWN OWNER, registered after the engine's hooks —
+      // the ordinary shape: the pool was built before the signal wiring.
+      process.on('SIGTERM', async () => {
+        await Promise.all([a.close(), b.close()])
+        // Stay alive a beat so the engine's deferred handler gets its turn and
+        // has to decide what to do about two already-closed brains.
+        await new Promise((r) => setTimeout(r, 1500))
+        report()
+        process.exit(0)
+      })
+      console.log('READY')
+      setInterval(() => {}, 1000)
+    `
+    const { child, output } = await startAndAwaitReady(scriptDir, script)
+
+    process.kill(-(child.pid as number), 'SIGTERM')
+    const code = await new Promise<number | null>((r) => child.on('exit', (c) => r(c)))
+    // The tsx wrapper's exit event and the grandchild that actually held the
+    // locks are asynchronous with each other — let its last writes land.
+    await new Promise<void>((r) => setTimeout(r, 750))
+    const out = output()
+
+    // The process shut down cleanly.
+    expect(code, `child output:\n${out}`).toBe(0)
+
+    // EXACTLY ONE close per brain — entered once, body run once. A second
+    // entry would mean the engine's handler closed a brain its owner was
+    // already closing; a second body would mean close() is not single-flight.
+    const { entries, bodies, releases } = readResult(resultPath, out)
+    expect(entries).toEqual({ a: 1, b: 1 })
+    expect(bodies).toEqual({ a: 1, b: 1 })
+    // ...and the writer lock was given up exactly once per brain. This is the
+    // assertion that fails on the old handler, which released the lock in its
+    // own `finally` on top of the owner's close doing the same — two owners.
+    expect(releases).toEqual({ a: 1, b: 1 })
+
+    // The engine's handler ran (it announced the signal) and stepped aside for
+    // both brains rather than touching them. setImmediate lands in the check
+    // phase of the same loop turn, so a close that has begun cannot have
+    // finished — it is still in flight when the handler looks.
+    expect(out).toContain('Shutdown signal received')
+    expect(out).toMatch(/2 Brainy instances are already closing/)
+
+    // Nothing was taken out from under the owner, and nothing failed.
+    expect(out).not.toMatch(/Writer fence lost/i)
+    expect(out).not.toMatch(/Failed to (flush|close) one Brainy instance/i)
+
+    // Both durability markers, both brains: the writer lock's clean-close
+    // record and the generation store's clean-shutdown marker.
+    for (const dir of [dirA, dirB]) {
+      expect(existsSync(closeRecordPath(dir)), `clean-close record missing in ${dir}`).toBe(true)
+      expect(cleanShutdownWritten(dir), `clean-shutdown marker missing in ${dir}`).toBe(true)
+    }
+
+    // And the next open adopts instead of folding.
+    await expectCleanReopen(dirA)
+    await expectCleanReopen(dirB)
+  }, 240_000)
+
+  it('(b) with no host owner the engine closes every instance the same way', async () => {
+    const script = `
+      import { writeFileSync as __writeFileSync } from 'node:fs'
+      import { Brainy } from ${JSON.stringify(BRAINY_SRC)}
+      const a = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: ${JSON.stringify(dirA)} } })
+      const b = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: ${JSON.stringify(dirB)} } })
+      await a.init()
+      await b.init()
+      await a.add({ data: 'row in brain a', type: 'concept' })
+      await b.add({ data: 'row in brain b', type: 'concept' })
+      ${childCounters(resultPath)}
+      instrument('a', a)
+      instrument('b', b)
+      process.on('exit', report)
+      console.log('READY')
+      setInterval(() => {}, 1000)
+    `
+    const { child, output } = await startAndAwaitReady(scriptDir, script)
+
+    process.kill(-(child.pid as number), 'SIGTERM')
+    const code = await new Promise<number | null>((r) => child.on('exit', (c) => r(c)))
+    // The tsx wrapper's exit event and the grandchild that actually held the
+    // locks are asynchronous with each other — let its last writes land.
+    await new Promise<void>((r) => setTimeout(r, 750))
+    const out = output()
+
+    expect(code, `child output:\n${out}`).toBe(0)
+
+    // The engine owned this shutdown: one close per brain, through close().
+    const { entries, bodies, releases } = readResult(resultPath, out)
+    expect(entries).toEqual({ a: 1, b: 1 })
+    expect(bodies).toEqual({ a: 1, b: 1 })
+    expect(releases).toEqual({ a: 1, b: 1 })
+    expect(out).toContain('Shutdown signal received')
+    expect(out).toMatch(/Flushed successfully \(2 instances\)/)
+    expect(out).not.toMatch(/Writer fence lost/i)
+    expect(out).not.toMatch(/Failed to (flush|close) one Brainy instance/i)
+
+    for (const dir of [dirA, dirB]) {
+      expect(existsSync(closeRecordPath(dir)), `clean-close record missing in ${dir}`).toBe(true)
+      expect(cleanShutdownWritten(dir), `clean-shutdown marker missing in ${dir}`).toBe(true)
+    }
+
+    await expectCleanReopen(dirA)
+    await expectCleanReopen(dirB)
+  }, 240_000)
+
+  it('(c) two concurrent close() callers share ONE execution, and both settle', async () => {
+    const brain = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dirA } })
+    await brain.init()
+    await brain.add({ data: 'one row', type: NounType.Concept })
+
+    const inner = brain as unknown as { closeDurableSteps: () => Promise<void> }
+    const durable = inner.closeDurableSteps.bind(inner)
+    let bodies = 0
+    inner.closeDurableSteps = () => { bodies++; return durable() }
+
+    expect(brain.isClosing).toBe(false)
+    expect(brain.isClosed).toBe(false)
+
+    const first = brain.close()
+    // The state is observable IMMEDIATELY — a signal handler that yields a
+    // tick and comes back must not read a stale "not yet".
+    expect(brain.isClosing).toBe(true)
+    const second = brain.close()
+    expect(first === second, 'concurrent callers must share the one promise').toBe(true)
+
+    await Promise.all([first, second])
+    expect(bodies).toBe(1)
+    expect(brain.isClosed).toBe(true)
+
+    // A caller arriving after the close finished gets the same settled answer,
+    // and nothing runs again.
+    await brain.close()
+    expect(bodies).toBe(1)
+
+    expect(existsSync(closeRecordPath(dirA))).toBe(true)
+    expect(cleanShutdownWritten(dirA)).toBe(true)
+  }, 120_000)
+
+  it('(d) N kicks during a running flush arm exactly one follow-up, never a second flush', async () => {
+    const brain = new Brainy({ requireSubtype: false, storage: { type: 'filesystem', path: dirA } })
+    await brain.init()
+
+    const inner = brain as unknown as {
+      _flushBodyRuns: number
+      _flushConcurrencyPeak: number
+      _flushInFlight: Promise<void> | null
+      _flushQueued: Promise<void> | null
+      _persistBackgroundFlight: Promise<void> | null
+      metadataIndex: { flush: () => Promise<void> }
+      kickBackgroundFlush: (reason: 'threshold' | 'idle') => void
+    }
+
+    // Widen the flush body's window so the kicks land INSIDE it — the
+    // production shape, where two flushes overlapped 3s apart.
+    const metaFlush = inner.metadataIndex.flush.bind(inner.metadataIndex)
+    inner.metadataIndex.flush = async () => {
+      await new Promise((r) => setTimeout(r, 400))
+      return metaFlush()
+    }
+
+    await brain.add({ data: 'a write to flush', type: NounType.Concept })
+    const runsBefore = inner._flushBodyRuns
+
+    const leader = brain.flush()
+    await new Promise((r) => setTimeout(r, 50)) // the leader is inside its body
+    expect(inner._flushInFlight, 'a flush is running').not.toBeNull()
+
+    // The cadence kicks — the door named in the defect — plus direct callers
+    // (an application flush, the cross-process flush-request watcher).
+    for (let i = 0; i < 5; i++) inner.kickBackgroundFlush('threshold')
+    const direct = [brain.flush(), brain.flush(), brain.flush()]
+
+    // EXACTLY ONE follow-up is armed, however many callers arrived.
+    expect(inner._flushQueued, 'the eight kicks armed one follow-up').not.toBeNull()
+
+    await Promise.all([leader, ...direct, inner._persistBackgroundFlight ?? Promise.resolve()])
+
+    // One leader + one follow-up. Not nine, and never two at once.
+    expect(inner._flushBodyRuns - runsBefore).toBe(2)
+    expect(inner._flushConcurrencyPeak).toBe(1)
+    expect(inner._flushInFlight).toBeNull()
+    expect(inner._flushQueued).toBeNull()
+
+    inner.metadataIndex.flush = metaFlush
+    await brain.close()
+  }, 120_000)
+})

tests/integration/storage-batch-operations.test.ts

@@ -95,7 +95,13 @@ describe('Storage-Level Batch Operations v5.12.0', () => {
       expect(entity?.vector?.length).toBeGreaterThan(0)
     })
 
-    it('should be faster than individual gets for large batches', async () => {
+    it('should be faster than individual gets for large batches', async (ctx) => {
+      // Wall-clock RATIO assertion — belongs to the perf lane (npm run
+      // test:perf), not the correctness gate: under the exclusive release
+      // gate this flaked when individual gets got faster on their own
+      // (open-path/hydration changes), not because batchGet regressed.
+      ctx.skip(!process.env.BRAINY_PERF_LANE, 'timing-ratio assertion — runs only under the perf lane (npm run test:perf)')
+
       // Create 100 entities
       const ids: string[] = []
       for (let i = 0; i < 100; i++) {

tests/integration/transact-edge-delete-bigint-aliasing.test.ts

@@ -0,0 +1,184 @@
+/**
+ * @module tests/integration/transact-edge-delete-bigint-aliasing
+ * @description Regression for a fleet-adoption blocker: ANY edge delete
+ * inside `transact()` — a direct unrelate or a noun-remove's cascade —
+ * aborted with the metadata seam's BigInt JSON-guard error on a strict
+ * (native) metadata provider.
+ *
+ * The aliasing chain: `planTxUnrelate`/the remove-cascade pass the SAME verb
+ * object to the graph-retraction op and the metadata-retraction op. The
+ * metadata leg's JSON-safe wrap ran at PLAN time, when the verb was still
+ * clean — so it returned the same reference. At EXECUTE time the graph op
+ * runs first and `resolveVerbEndpointInts` mirrors BigInt
+ * `sourceInt`/`targetInt` onto the shared object (deliberately deferred for
+ * same-batch forward refs — see transact-forward-ref-graph.test.ts); the
+ * metadata op then crossed the seam with the polluted object. Direct
+ * `unrelate()` resolves ints at BUILD time, before its sanitize, which is why
+ * only the transact() shapes ever hit it.
+ *
+ * Fix under pin: the JSON-safe view is taken AT THE CROSSING — inside the
+ * metadata-index operations' execute/rollback — so no plan-vs-execute
+ * ordering can bypass it. The JS baseline index tolerates BigInts (it would
+ * mask the bug), so these pins SPY on the seam and assert what actually
+ * crossed, exactly as a strict native provider would judge it.
+ */
+import { describe, it, expect, beforeEach, afterEach } from 'vitest'
+import * as fs from 'node:fs'
+import * as os from 'node:os'
+import * as path from 'node:path'
+import { Brainy } from '../../src/brainy.js'
+import { NounType, VerbType } from '../../src/types/graphTypes.js'
+import {
+  AddToMetadataIndexOperation,
+  RemoveFromMetadataIndexOperation
+} from '../../src/transaction/operations/index.js'
+
+let seq = 0
+const freshId = (): string =>
+  `00000000-0000-4000-8000-${(++seq).toString(16).padStart(12, '0')}`
+
+/** Top-level BigInt-valued keys of a candidate seam crossing (the guard's law). */
+const bigintKeys = (metadata: unknown): string[] => {
+  if (metadata === null || typeof metadata !== 'object') return []
+  return Object.entries(metadata as Record<string, unknown>)
+    .filter(([, v]) => typeof v === 'bigint')
+    .map(([k]) => k)
+}
+
+describe('transact() edge deletes never carry BigInt across the metadata seam', () => {
+  let dir: string
+  let brain: any
+  let crossings: Array<{ door: string; id: string; keys: string[] }>
+
+  beforeEach(async () => {
+    process.env.BRAINY_DETERMINISTIC_EMBEDDINGS = 'true'
+    dir = fs.mkdtempSync(path.join(os.tmpdir(), 'brainy-tx-bigint-'))
+    brain = new Brainy({
+      requireSubtype: false,
+      storage: { type: 'filesystem', path: dir },
+      dimensions: 384,
+      silent: true
+    })
+    await brain.init()
+
+    // Spy on the seam the way a strict native provider judges it: record the
+    // BigInt-valued top-level keys of every metadata argument that crosses.
+    // The JS baseline index tolerates BigInts, so without this the baseline
+    // run would green a shape the native pair aborts on.
+    crossings = []
+    const index = brain.metadataIndex
+    for (const door of ['addToIndex', 'removeFromIndex'] as const) {
+      const real = index[door].bind(index)
+      index[door] = (id: string, metadata: unknown, ...rest: unknown[]) => {
+        crossings.push({ door, id, keys: bigintKeys(metadata) })
+        return real(id, metadata, ...rest)
+      }
+    }
+  })
+
+  afterEach(async () => {
+    await brain.close()
+    fs.rmSync(dir, { recursive: true, force: true })
+  })
+
+  it('CASE 1 (the fleet repro): relate, then transact([{op: unrelate}])', async () => {
+    const a = await brain.add({ id: freshId(), data: 'a', type: NounType.Thing })
+    const b = await brain.add({ id: freshId(), data: 'b', type: NounType.Thing })
+    const verbId = await brain.relate({ from: a, to: b, type: VerbType.RelatedTo })
+
+    crossings.length = 0
+    await brain.transact([{ op: 'unrelate', id: verbId }])
+
+    const polluted = crossings.filter((c) => c.keys.length > 0)
+    expect(polluted).toEqual([])
+    expect(await brain.storage.getVerb(verbId)).toBeFalsy()
+  })
+
+  it('CASE 2 (the cascade shape): transact([{op: remove}]) cascading edge deletes', async () => {
+    const a = await brain.add({ id: freshId(), data: 'a', type: NounType.Thing })
+    const b = await brain.add({ id: freshId(), data: 'b', type: NounType.Thing })
+    const c = await brain.add({ id: freshId(), data: 'c', type: NounType.Thing })
+    const ab = await brain.relate({ from: a, to: b, type: VerbType.RelatedTo })
+    const ca = await brain.relate({ from: c, to: a, type: VerbType.RelatedTo })
+
+    crossings.length = 0
+    await brain.transact([{ op: 'remove', id: a }])
+
+    const polluted = crossings.filter((c2) => c2.keys.length > 0)
+    expect(polluted).toEqual([])
+    expect(await brain.get(a)).toBeFalsy()
+    expect(await brain.storage.getVerb(ab)).toBeFalsy()
+    expect(await brain.storage.getVerb(ca)).toBeFalsy()
+  })
+
+  it('CASE 3 (one batch, both legs): adds + relate + unrelate of a pre-existing edge', async () => {
+    const a = await brain.add({ id: freshId(), data: 'a', type: NounType.Thing })
+    const b = await brain.add({ id: freshId(), data: 'b', type: NounType.Thing })
+    const old = await brain.relate({ from: a, to: b, type: VerbType.RelatedTo })
+
+    const x = freshId()
+    crossings.length = 0
+    await brain.transact([
+      { op: 'add', id: x, data: 'x', type: NounType.Thing },
+      { op: 'relate', from: a, to: x, type: VerbType.RelatedTo },
+      { op: 'unrelate', id: old }
+    ])
+
+    const polluted = crossings.filter((c) => c.keys.length > 0)
+    expect(polluted).toEqual([])
+    expect(await brain.storage.getVerb(old)).toBeFalsy()
+    const edges = await brain.related({ from: a })
+    expect(edges.length).toBe(1)
+    expect(edges[0].id).not.toBe(old)
+  })
+})
+
+describe('the metadata-index operations sanitize at the crossing, not at construction', () => {
+  /** A strict seam: refuses BigInts exactly as the native provider does. */
+  const strictIndex = () => {
+    const seen: Array<{ door: string; keys: string[] }> = []
+    const judge = (door: string, metadata: unknown) => {
+      const keys = bigintKeys(metadata)
+      seen.push({ door, keys })
+      if (keys.length > 0) {
+        throw new Error(
+          `${door}: the metadata object violates the provider seam's JSON ` +
+            `contract — BigInt at ${keys.join(', ')}.`
+        )
+      }
+    }
+    return {
+      seen,
+      addToIndex: async (_id: string, metadata: unknown) => judge('addToIndex', metadata),
+      removeFromIndex: async (_id: string, metadata: unknown) => judge('removeFromIndex', metadata)
+    }
+  }
+
+  it('RemoveFromMetadataIndexOperation: entity mutated AFTER construction still crosses clean', async () => {
+    const index = strictIndex()
+    const verb: Record<string, unknown> = { id: 'v1', sourceId: 'a', targetId: 'b' }
+    const op = new RemoveFromMetadataIndexOperation(index as any, 'v1', verb, () => 7n)
+
+    // The graph leg's execute-time endpoint resolution, simulated: the shared
+    // object is polluted between plan and execute.
+    verb.sourceInt = 800_000n
+    verb.targetInt = 800_001n
+
+    const rollback = await op.execute()
+    await rollback()
+    expect(index.seen.map((s) => s.keys)).toEqual([[], []])
+  })
+
+  it('AddToMetadataIndexOperation: same law on the add leg and its rollback', async () => {
+    const index = strictIndex()
+    const verb: Record<string, unknown> = { id: 'v2', sourceId: 'a', targetId: 'b' }
+    const op = new AddToMetadataIndexOperation(index as any, 'v2', verb, () => 7n)
+
+    verb.sourceInt = 800_000n
+    verb.targetInt = 800_001n
+
+    const rollback = await op.execute()
+    await rollback()
+    expect(index.seen.map((s) => s.keys)).toEqual([[], []])
+  })
+})

tests/integration/vfs-containment-batched.test.ts

@@ -0,0 +1,115 @@
+/**
+ * @module tests/integration/vfs-containment-batched
+ * @description repairContainment costs O(edges/page) graph calls, not O(entities) (10.4.9 train).
+ *
+ * Pass 2 used to issue one awaited `related({ to })` per VFS entity — minutes
+ * of serialized graph calls on large brains. Now one paged walk over every
+ * Contains edge feeds an in-memory group-by-target, and only actual defects
+ * mutate. These pins hold the verdicts (duplicate removed, stale parent
+ * removed, missing edge restored, user knowledge edges untouched) AND the
+ * cost shape (related() call count independent of the entity count).
+ */
+import { describe, it, expect, beforeAll, afterAll, vi } from 'vitest'
+import { Brainy } from '../../src/brainy'
+import { NounType, VerbType } from '../../src/types/graphTypes'
+
+const FILES = 60
+
+describe('repairContainment: batched pass 2', () => {
+  let brain: Brainy<any>
+  let result: { removed: number; restored: number }
+  let relatedCalls = 0
+
+  beforeAll(async () => {
+    brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    await brain.init()
+    const vfs = (brain as any).vfs ?? (brain as any)._vfs
+    expect(vfs).toBeTruthy()
+    await vfs.init()
+
+    // A directory and FILES entries under it, wired as real VFS rows.
+    const mkNode = async (id: string, path: string, vfsType: string): Promise<void> => {
+      await brain.add({
+        id,
+        data: `vfs node ${path}`,
+        type: NounType.File,
+        visibility: 'system',
+        metadata: { vfsType, path }
+      })
+    }
+    await mkNode('dir', '/docs', 'directory')
+    const rootId = vfs.rootEntityId ?? (await vfs.initializeRoot?.())
+    if (rootId) {
+      await brain.relate({
+        from: rootId,
+        to: 'dir',
+        type: VerbType.Contains,
+        subtype: 'vfs-contains',
+        metadata: { isVFS: true }
+      })
+    }
+    for (let i = 0; i < FILES; i++) {
+      await mkNode(`f-${i}`, `/docs/f-${i}.md`, 'file')
+      if (i === 0) continue // f-0: MISSING edge — must be restored
+      await brain.relate({
+        from: 'dir',
+        to: `f-${i}`,
+        type: VerbType.Contains,
+        subtype: 'vfs-contains',
+        metadata: { isVFS: true }
+      })
+    }
+    // NOTE: relate() is idempotent for an identical from/to/type, so a true
+    // duplicate (a concurrent-writer artifact) cannot be seeded through the
+    // public API — the duplicate branch is covered by the tree-correctness
+    // pin below, which proves at most one vfs edge survives per file.
+    // f-2: STALE parent edge (from a sibling file) — must be removed.
+    await brain.relate({
+      from: 'f-3',
+      to: 'f-2',
+      type: VerbType.Contains,
+      subtype: 'vfs-contains',
+      metadata: { isVFS: true }
+    })
+    // A USER knowledge Contains edge (not vfs-flagged) — must be untouched.
+    await brain.relate({ from: 'f-4', to: 'f-5', type: VerbType.Contains })
+
+    const spy = vi.spyOn(brain, 'related')
+    result = await vfs.repairContainment()
+    relatedCalls = spy.mock.calls.length
+    spy.mockRestore()
+  })
+
+  afterAll(async () => {
+    brain = null as any
+  })
+
+  it('restores the missing edge and removes the stale parent — exactly', () => {
+    expect(result.restored).toBe(1) // f-0's missing edge
+    expect(result.removed).toBe(1) // f-2's stale parent (f-3 → f-2)
+  })
+
+  it('the repaired tree is correct: every file has exactly one vfs edge from its dir', async () => {
+    for (let i = 0; i < 6; i++) {
+      const incoming = await brain.related({ to: `f-${i}`, type: VerbType.Contains })
+      const vfsEdges = incoming.filter(
+        (e) => e.subtype === 'vfs-contains' || (e.metadata as any)?.isVFS === true
+      )
+      expect(vfsEdges, `f-${i}`).toHaveLength(1)
+    }
+  })
+
+  it('never touches user knowledge edges', async () => {
+    const incoming = await brain.related({ to: 'f-5', type: VerbType.Contains })
+    const user = incoming.filter(
+      (e) => e.subtype !== 'vfs-contains' && (e.metadata as any)?.isVFS !== true
+    )
+    expect(user).toHaveLength(1)
+  })
+
+  it('cost shape: related() calls do not scale with the entity count', () => {
+    // One paged type-only walk (~E/1000 pages) — with 60+ entities the old
+    // shape issued 60+ calls; the new one a handful. Bound generously.
+    expect(relatedCalls).toBeLessThanOrEqual(5)
+  })
+})

tests/unit/brainy/batch-operations.test.ts

@@ -113,7 +113,12 @@ describe('Brainy Batch Operations', () => {
         items: Array.from({ length: 100 }, (_, i) => ({
           data: `Bulk ${i}`,
           type: NounType.Thing,
-          metadata: { counter: 0 }
+          metadata: { counter: 0 },
+          // This test exercises updateMany's batching, not embedding — the
+          // sanctioned "unvectored" `[]` shape (see
+          // tests/integration/index-skips-unvectored.test.ts) skips the
+          // real embedder entirely.
+          vector: []
         }))
       })
       const manyIds = manyResult.successful
@@ -274,7 +279,12 @@ describe('Brainy Batch Operations', () => {
       const manyResult = await brain.addMany({
         items: Array.from({ length: 100 }, (_, i) => ({
           data: `Bulk Delete ${i}`,
-          type: NounType.Thing
+          type: NounType.Thing,
+          // This test exercises removeMany's batching, not embedding — the
+          // sanctioned "unvectored" `[]` shape (see
+          // tests/integration/index-skips-unvectored.test.ts) skips the
+          // real embedder entirely.
+          vector: []
         }))
       })
       const manyIds = manyResult.successful
@@ -545,10 +555,18 @@ describe('Brainy Batch Operations', () => {
     
     it('should validate batch size limits', async () => {
       // Try to add a large batch (reduced from 10000 to 1000 for reasonable test time)
+      // This test validates the batch SIZE law, not embeddings — items carry
+      // the sanctioned "unvectored" `[]` shape (see
+      // tests/integration/index-skips-unvectored.test.ts) so addMany's batch
+      // embedder is never invoked; 1000 real embeddings under the root
+      // vitest config (which does not mock the embedder) is a 60-180s
+      // budget flake waiting to happen, not a defect in what this test
+      // actually asserts.
       const largeCount = 1000
       const largeItems = Array.from({ length: largeCount }, (_, i) => ({
         data: `Large ${i}`,
-        type: NounType.Thing
+        type: NounType.Thing,
+        vector: []
       }))
 
       try {
@@ -560,12 +578,7 @@ describe('Brainy Batch Operations', () => {
         // Might throw if there's a limit
         expect(error).toBeDefined()
       }
-      // order-of-magnitude guard: this test batches 20x the item count of the
-      // sibling "perform better" test above (worst measured 11.9s for 50
-      // items on CPU-only honest iron); the prior 60s timeout was itself
-      // observed being hit, so this is 3x that floor rather than a scaled
-      // extrapolation, to leave real headroom for run-to-run variance
-    }, 180000)
+    })
     
     it('should provide meaningful error messages', async () => {
       try {

tests/unit/brainy/flush-single-flight.test.ts

@@ -0,0 +1,175 @@
+/**
+ * @module tests/unit/brainy/flush-single-flight
+ * @description THE FLUSH GATE NEVER STRANDS A WAITER.
+ *
+ * The gate serialises flushes: one body runs, at most one waits. The failure
+ * mode that shape invites is a promise CYCLE — a queued follow-up expressed as
+ * `leader.then(() => this.flush())` is settled only by resolving the promise
+ * the leader is being awaited through, so anything that awaits `flush()` from
+ * inside a flush body closes the graph on itself and nobody ever resolves.
+ * That is an unbounded hang, not a slow flush, and it presents exactly like a
+ * test timing out inside a bulk write.
+ *
+ * The gate therefore settles its waiter from the MACHINE (a bare deferred
+ * promoted in the leader's `finally`), never from a chain. The laws pinned
+ * here, each on a path that must settle the waiter:
+ *
+ *   (a) many callers during one running flush → one body, one follow-up, and
+ *       EVERY caller resolves within a bound;
+ *   (b) the leader REJECTS → its own caller rejects, and the queued caller is
+ *       still run and still settled;
+ *   (c) the promoted follow-up itself rejects → its waiter rejects (settled,
+ *       not stranded) and the gate is left open for the next flush;
+ *   (d) the leader's promise does not wait for its follower.
+ */
+
+import { describe, it, expect, afterEach } from 'vitest'
+import { Brainy } from '../../../src/brainy'
+import { NounType } from '../../../src/types/graphTypes'
+
+type GateInternals = {
+  _flushInFlight: Promise<void> | null
+  _flushQueued: Promise<void> | null
+  _flushBodyRuns: number
+  _flushConcurrencyPeak: number
+  _flushSteps: () => Promise<void>
+  kickBackgroundFlush: (reason: 'threshold' | 'idle') => void
+}
+
+/** Fail loudly rather than hanging the suite: a stranded waiter never settles. */
+function withinBound<T>(p: Promise<T>, ms: number, what: string): Promise<T> {
+  let timer: ReturnType<typeof setTimeout>
+  return Promise.race([
+    p,
+    new Promise<never>((_, reject) => {
+      timer = setTimeout(() => reject(new Error(`${what} did not settle within ${ms}ms`)), ms)
+    })
+  ]).finally(() => clearTimeout(timer)) as Promise<T>
+}
+
+describe('the flush gate settles every waiter', () => {
+  const brains: Brainy<any>[] = []
+
+  afterEach(async () => {
+    for (const b of brains.splice(0)) {
+      try { await b.close() } catch { /* already closed */ }
+    }
+  })
+
+  async function openBrain(): Promise<Brainy<any>> {
+    const brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
+    brains.push(brain)
+    await brain.init()
+    await brain.add({ data: 'a write, so a flush has work', type: NounType.Thing })
+    return brain
+  }
+
+  it('(a) every caller arriving during one flush resolves, and only one follows', async () => {
+    const brain = await openBrain()
+    const inner = brain as unknown as GateInternals
+
+    const realSteps = inner._flushSteps.bind(inner)
+    inner._flushSteps = async () => {
+      await new Promise((r) => setTimeout(r, 120))
+      return realSteps()
+    }
+
+    const runsBefore = inner._flushBodyRuns
+    const leader = brain.flush()
+    await new Promise((r) => setTimeout(r, 20))
+
+    const joiners = [brain.flush(), brain.flush(), brain.flush(), brain.flush()]
+    for (let i = 0; i < 4; i++) inner.kickBackgroundFlush('threshold')
+    expect(inner._flushQueued, 'exactly one waiter is queued').not.toBeNull()
+
+    await withinBound(Promise.all([leader, ...joiners]), 15_000, 'the flush callers')
+
+    expect(inner._flushBodyRuns - runsBefore).toBe(2)
+    expect(inner._flushConcurrencyPeak).toBe(1)
+    expect(inner._flushQueued).toBeNull()
+  })
+
+  it('(b) a leader that REJECTS still runs and settles the queued waiter', async () => {
+    const brain = await openBrain()
+    const inner = brain as unknown as GateInternals
+
+    const realSteps = inner._flushSteps.bind(inner)
+    let call = 0
+    inner._flushSteps = async () => {
+      call++
+      await new Promise((r) => setTimeout(r, 80))
+      if (call === 1) throw new Error('injected: the leader flush failed')
+      return realSteps()
+    }
+
+    const leader = brain.flush()
+    await new Promise((r) => setTimeout(r, 20))
+    const queued = brain.flush()
+
+    await expect(leader).rejects.toThrow(/injected: the leader flush failed/)
+    // The waiter is NOT collateral damage of the leader's failure: it gets its
+    // own run, and it settles.
+    await withinBound(queued, 15_000, 'the queued waiter after a failed leader')
+    expect(call).toBe(2)
+    expect(inner._flushQueued).toBeNull()
+    expect(inner._flushInFlight).toBeNull()
+  })
+
+  it('(c) a promoted follow-up that rejects settles its waiter and opens the gate', async () => {
+    const brain = await openBrain()
+    const inner = brain as unknown as GateInternals
+
+    const realSteps = inner._flushSteps.bind(inner)
+    let call = 0
+    inner._flushSteps = async () => {
+      call++
+      await new Promise((r) => setTimeout(r, 80))
+      if (call === 2) throw new Error('injected: the follow-up flush failed')
+      return realSteps()
+    }
+
+    const leader = brain.flush()
+    await new Promise((r) => setTimeout(r, 20))
+    const queued = brain.flush()
+
+    await withinBound(leader, 15_000, 'the leader')
+    await withinBound(
+      expect(queued).rejects.toThrow(/injected: the follow-up flush failed/),
+      15_000,
+      'the rejected follow-up'
+    )
+    // The gate is open: a later flush still runs.
+    inner._flushSteps = realSteps
+    await brain.add({ data: 'another write', type: NounType.Thing })
+    await withinBound(brain.flush(), 15_000, 'the flush after a failed follow-up')
+    expect(inner._flushInFlight).toBeNull()
+    expect(inner._flushQueued).toBeNull()
+  })
+
+  it('(d) the leader does not wait for its follower', async () => {
+    const brain = await openBrain()
+    const inner = brain as unknown as GateInternals
+
+    const realSteps = inner._flushSteps.bind(inner)
+    let call = 0
+    inner._flushSteps = async () => {
+      call++
+      // The follow-up is deliberately far slower than the leader.
+      await new Promise((r) => setTimeout(r, call === 1 ? 60 : 600))
+      return realSteps()
+    }
+
+    const leader = brain.flush()
+    await new Promise((r) => setTimeout(r, 20))
+    const queued = brain.flush()
+
+    const t0 = Date.now()
+    await withinBound(leader, 15_000, 'the leader')
+    const leaderWall = Date.now() - t0
+    // If the leader awaited its follower it could not return before the
+    // follower's own 600ms body had run.
+    expect(leaderWall).toBeLessThan(500)
+
+    await withinBound(queued, 15_000, 'the follower')
+  })
+})

tests/unit/db/generation-segments.test.ts

@@ -147,4 +147,119 @@ describe('db/GenerationSegmentStore — the D1+D3 packed tier', () => {
     await expect(store.fold([gen(4), gen(4)])).rejects.toThrow(/strictly ascending/)
     await expect(store.fold([])).rejects.toThrow(/at least one generation/)
   })
+
+  // ==========================================================================
+  // THE DENSITY LAW
+  // ==========================================================================
+  //
+  // A sealed segment declares a CONTIGUOUS range and every reader treats that
+  // range as containment. Folding a sparse batch therefore makes the segment
+  // claim generations it does not hold — and because `open()` merges declared
+  // ranges back into committedRanges, the hole is re-admitted as committed
+  // history and every later maintenance pass fails asking for a frame that was
+  // never written. That is the "generation N is inside sealed segment
+  // seg-....bgs's declared range but has no frame — packed history is damaged"
+  // narration seen on every run of the affected stores.
+
+  it('fold REFUSES a batch with a hole — a dense range may not be declared over sparse input', async () => {
+    await expect(store.fold([gen(1), gen(2), gen(4)])).rejects.toThrow(
+      /not contiguous: 2 → 4 skips 1 generation/
+    )
+    // The refusal loses nothing: no segment was sealed, so the generations
+    // stay in the live tier and the next pass folds them correctly.
+    expect(store.segments()).toHaveLength(0)
+    expect(store.hasGeneration(1)).toBe(false)
+  })
+
+  it('a wider gap names how many generations it would have swallowed', async () => {
+    await expect(store.fold([gen(10), gen(20)])).rejects.toThrow(
+      /not contiguous: 10 → 20 skips 9 generation\(s\)/
+    )
+  })
+
+  it('two contiguous runs folded separately declare honest ranges', async () => {
+    // What the caller now does instead of folding across the gap.
+    const a = await store.fold([gen(1), gen(2), gen(3)])
+    const b = await store.fold([gen(7), gen(8)])
+    expect(a).toMatchObject({ firstGeneration: 1, lastGeneration: 3, frames: 3 })
+    expect(b).toMatchObject({ firstGeneration: 7, lastGeneration: 8, frames: 2 })
+    // The gap is honestly outside the packed tier.
+    for (const g of [4, 5, 6]) expect(store.hasGeneration(g)).toBe(false)
+    for (const g of [1, 2, 3, 7, 8]) expect(store.hasGeneration(g)).toBe(true)
+    expect(await store.actualRanges()).toEqual([
+      [1, 3],
+      [7, 8]
+    ])
+  })
+
+  it('actualRanges() is exact and I/O-free for dense segments', async () => {
+    await store.fold([gen(1), gen(2)])
+    await store.fold([gen(3), gen(4)])
+    // Adjacent dense segments each contribute their declared range.
+    expect(await store.actualRanges()).toEqual([
+      [1, 2],
+      [3, 4]
+    ])
+  })
+
+  // ---- pre-existing damage: a store sealed by the old writer ----------------
+
+  /**
+   * Seal a SPARSE segment the way the pre-fix writer did: write the bytes and
+   * sidecar for a contiguous run, then rewrite the manifest so the segment
+   * declares a wider range than the frames it holds. This reproduces on disk
+   * exactly what the affected stores carry, without needing the old code.
+   */
+  const sealSparseSegment = async (): Promise<void> => {
+    await store.fold([gen(1), gen(2), gen(3)])
+    const manifest = (await storage.readRawObject(`${SEGMENTS_PREFIX}/manifest.json`)) as any
+    // Declare 1..5 while holding frames for 1..3 — generations 4 and 5 become
+    // holes inside a sealed range.
+    manifest.segments[0].lastGeneration = 5
+    await storage.writeRawObject(`${SEGMENTS_PREFIX}/manifest.json`, manifest)
+  }
+
+  it('a pre-existing sparse segment reports its holes as UNPACKED, not as damage', async () => {
+    await sealSparseSegment()
+    const reopened = new GenerationSegmentStore(storage as any)
+    await reopened.open()
+
+    // The frames it really holds still serve, byte-faithfully.
+    expect((await reopened.readDelta(2))?.timestamp).toBe(1_700_000_000_002)
+    expect(await reopened.readRecords(3)).toHaveLength(2)
+
+    // The holes answer "not packed" instead of throwing. This is the fix for
+    // the wedge: the old reader threw here on EVERY maintenance pass.
+    expect(await reopened.readDelta(4)).toBeNull()
+    expect(await reopened.readRecords(5)).toBeNull()
+  })
+
+  it('actualRanges() excludes the holes so they are never re-admitted as committed', async () => {
+    await sealSparseSegment()
+    const reopened = new GenerationSegmentStore(storage as any)
+    await reopened.open()
+    // Declared 1..5; actually holds 1..3. The store seeds committedRanges from
+    // THIS, so generations 4 and 5 never become committed history again.
+    expect(await reopened.actualRanges()).toEqual([[1, 3]])
+  })
+
+  it('a DENSE segment missing a frame is still loud damage', async () => {
+    // The other side of the branch: when the manifest claims a complete span,
+    // a missing frame means the manifest and sidecar disagree — real damage,
+    // and it must not be quietly downgraded to "unpacked".
+    await store.fold([gen(1), gen(2), gen(3)])
+    const idxPath = `${SEGMENTS_PREFIX}/seg-${String(1).padStart(20, '0')}.idx`
+    const raw = (await storage.readRawBytes(idxPath))!
+    const { decode, encode } = await import('@msgpack/msgpack')
+    const idx = decode(raw) as any
+    // Drop generation 2's entry while the manifest still declares 3 frames.
+    idx.generations = idx.generations.filter(([g]: [number]) => g !== 2)
+    await storage.writeRawBytes(idxPath, encode(idx))
+
+    const reopened = new GenerationSegmentStore(storage as any)
+    await reopened.open()
+    await expect(reopened.readDelta(2)).rejects.toThrow(
+      /manifest and the sidecar disagree; packed history is damaged/
+    )
+  })
 })

tests/unit/db/generationStore-commit-guard.test.ts

@@ -0,0 +1,254 @@
+/**
+ * @module tests/unit/db/generationStore-commit-guard
+ * @description Pins the commit-order guard on
+ * `GenerationStore.commitTransaction()` (`src/db/generationStore.ts`).
+ *
+ * `reservedGensAsc()`'s own doc comment states an invariant it never
+ * enforced: pending single-op generations are always greater than every
+ * committed one, because the store's only two sanctioned callers —
+ * `Brainy.transact()` and `Brainy.compactHistory()` — flush the pending tier
+ * before committing. Nothing stopped a caller from invoking
+ * `commitTransaction()` directly while single-ops were still buffered: the
+ * fresh commit would land in `committedRanges` ABOVE those lower,
+ * still-pending generations, so the committed-then-pending concatenation
+ * `reservedGensAsc()` yields is no longer ascending — and `resolveManyAt`
+ * (which walks committed ranges before pending ones) would silently report a
+ * WRONG before-image for a point-in-time read. `commitTransaction()` now
+ * refuses loudly (`PendingSingleOpsUnflushedError`) instead of assuming.
+ *
+ * Four pins:
+ * 1. A direct `commitTransaction()` call while single-ops are pending throws
+ *    and commits NOTHING.
+ * 2. The same commit succeeds once the pending tier is flushed first.
+ * 3. `Brainy.transact()` — which already flushes first — is unaffected
+ *    (mirrors `tests/unit/db/generation-chain.test.ts`'s `seedX()`/`bumpX()`
+ *    transact pin: add, then transact-update, generation advances by one
+ *    each time, the update lands).
+ * 4. `reservedGensAsc()` stays ascending across a real add+transact+delete
+ *    workload — proven by point-in-time reads (`asOf`) staying correct
+ *    throughout, which is exactly what an ordering break would corrupt.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest'
+import { MemoryStorage } from '../../../src/storage/adapters/memoryStorage.js'
+import {
+  GenerationStore,
+  GENERATIONS_PREFIX,
+  MANIFEST_PATH
+} from '../../../src/db/generationStore.js'
+import { PendingSingleOpsUnflushedError } from '../../../src/db/errors.js'
+import { Brainy } from '../../../src/index.js'
+import { NounType } from '../../../src/types/graphTypes.js'
+import { createTestConfig, generateTestVector } from '../../helpers/test-factory.js'
+
+/** Precomputed embedding so Brainy-level adds skip the (slow) embedding model —
+ *  these tests exercise the generation layer, not semantics. */
+const VEC = generateTestVector()
+
+// Entity ids must be UUID-shaped (the sharded storage layout derives the
+// shard from the UUID hex) — same fixture convention as generationStore.test.ts.
+const ID_A = '00000000-0000-4000-8000-0000000000aa'
+const ID_B = '00000000-0000-4000-8000-0000000000bb'
+
+/** Stored-metadata fixture in the canonical shape the live write paths use
+ *  (matches generationStore.test.ts's fixture exactly). */
+function metadataFixture(version: number): Record<string, unknown> {
+  return {
+    noun: NounType.Document,
+    subtype: 'note',
+    data: `payload-v${version}`,
+    version,
+    createdAt: 1000,
+    updatedAt: 1000 + version,
+    _rev: version
+  }
+}
+
+describe('db/GenerationStore — commitTransaction pending-tier guard (store level)', () => {
+  let storage: MemoryStorage
+  let store: GenerationStore
+
+  beforeEach(async () => {
+    storage = new MemoryStorage()
+    await storage.init()
+    store = new GenerationStore(storage)
+    await store.open()
+  })
+
+  /** Buffer one single-op generation via commitSingleOp WITHOUT flushing —
+   *  the pending tier that must be drained before commitTransaction(). */
+  async function pendingSingleOp(id: string, version: number): Promise<number> {
+    const { generation } = await store.commitSingleOp({
+      touched: { nouns: [id] },
+      execute: async () => {
+        await storage.saveNounMetadata(id, metadataFixture(version))
+      }
+    })
+    return generation
+  }
+
+  /** A direct transact commit — exactly what a caller bypassing
+   *  Brainy.transact()'s flush-first step would issue. */
+  function directCommit(id: string, version: number): Promise<{ generation: number; timestamp: number }> {
+    return store.commitTransaction({
+      touched: { nouns: [id], verbs: [] },
+      execute: async () => {
+        await storage.saveNounMetadata(id, metadataFixture(version))
+      }
+    })
+  }
+
+  it('PIN 1: refuses a direct commitTransaction() while single-ops are pending, and commits NOTHING', async () => {
+    const g1 = await pendingSingleOp(ID_A, 1)
+    expect(g1).toBe(1)
+    expect(store.committedGeneration()).toBe(0) // nothing flushed to disk yet
+
+    let caught: unknown
+    try {
+      await directCommit(ID_B, 1)
+      expect.unreachable('should have thrown PendingSingleOpsUnflushedError')
+    } catch (err) {
+      caught = err
+    }
+    expect(caught).toBeInstanceOf(PendingSingleOpsUnflushedError)
+    expect((caught as PendingSingleOpsUnflushedError).pendingCount).toBe(1)
+
+    // Nothing committed: the head + committed ranges are unchanged, and the
+    // counter never advanced for the refused attempt (the guard fires before
+    // a generation is even reserved).
+    expect(store.committedGeneration()).toBe(0)
+    expect(store.generation()).toBe(1) // still just the pending single-op's gen
+    expect(await storage.readRawObject(MANIFEST_PATH)).toBeNull()
+    // The guard fires BEFORE a generation is reserved (`gen = ++this.counter`
+    // never runs), so the refused attempt's would-be directory (generation 2,
+    // the next number after the pending single-op's 1) was never created.
+    expect(await storage.listRawObjects(`${GENERATIONS_PREFIX}/2`)).toEqual([])
+
+    // The refused write never touched canonical storage.
+    expect((await storage.readNounRaw(ID_B)).metadata).toBeNull()
+
+    // The pending tier itself is untouched by the refused attempt — flushing
+    // now still commits the ORIGINAL single-op cleanly.
+    await store.flushPendingSingleOps()
+    expect(store.committedGeneration()).toBe(1)
+    const atG0 = await store.resolveAt('noun', ID_A, 0)
+    expect(atG0).toEqual({ source: 'absent' }) // the create sentinel before g1's write
+  })
+
+  it('PIN 2: the same commit succeeds once the pending tier is flushed first', async () => {
+    await pendingSingleOp(ID_A, 1)
+    await expect(directCommit(ID_B, 1)).rejects.toBeInstanceOf(PendingSingleOpsUnflushedError)
+
+    await store.flushPendingSingleOps()
+    expect(store.committedGeneration()).toBe(1)
+
+    const { generation } = await directCommit(ID_B, 1)
+    expect(generation).toBe(2)
+    expect(store.committedGeneration()).toBe(2)
+    expect((await storage.readNounRaw(ID_B)).metadata).toMatchObject({ version: 1 })
+  })
+})
+
+describe('Brainy public API — commitTransaction pending-tier guard is behavior-neutral', () => {
+  let brain: Brainy
+
+  beforeEach(async () => {
+    brain = new Brainy(createTestConfig())
+    await brain.init()
+  })
+  afterEach(async () => {
+    await brain.close()
+  })
+
+  it('PIN 3: Brainy.transact() still commits normally over pending single-ops (mirrors generation-chain.test.ts\'s seedX()/bumpX() transact pin)', async () => {
+    const store = (brain as any).generationStore as GenerationStore
+    // Relative, not absolute: under the adopt-at-open default the open-time
+    // baseline backfill takes a generation of its own (see
+    // bounded-chains.test.ts's identical note), so the first user add is not
+    // necessarily generation 1.
+    const baseGen = brain.generation()
+    const baseCommitted = store.committedGeneration()
+
+    const id = await brain.add({
+      data: 'x',
+      type: NounType.Document,
+      subtype: 'note',
+      metadata: { v: 1 },
+      vector: VEC
+    })
+    // The add is a pending single-op generation — NOT yet flushed.
+    expect(brain.generation()).toBe(baseGen + 1)
+    expect(store.committedGeneration()).toBe(baseCommitted)
+
+    // Brainy.transact() flushes the pending tier FIRST (src/brainy.ts:
+    // `await this.generationStore.flushPendingSingleOps()`, immediately
+    // before its `generationStore.commitTransaction()` call), so the guard
+    // never fires on this path — same shape as generation-chain.test.ts's
+    // seedX() (add) → bumpX() (transact update) → generation advances by one.
+    const db = await brain.transact([{ op: 'update', id, metadata: { v: 2 } }])
+    await db.release()
+
+    expect(brain.generation()).toBe(baseGen + 2)
+    expect(store.committedGeneration()).toBe(baseGen + 2) // the flushed add + the transact update
+    const entity = (await brain.get(id)) as any
+    expect(entity.metadata.v).toBe(2)
+  })
+
+  it('PIN 4: reservedGensAsc() stays ascending across a real add+transact+delete workload — point-in-time reads stay correct', async () => {
+    const store = (brain as any).generationStore as GenerationStore
+    const baseGen = brain.generation()
+    const baseCommitted = store.committedGeneration()
+
+    const idX = await brain.add({
+      data: 'x',
+      type: NounType.Document,
+      subtype: 'note',
+      metadata: { v: 1 },
+      vector: VEC
+    })
+    expect(brain.generation()).toBe(baseGen + 1) // pending (un-flushed)
+
+    const idY = await brain.add({
+      data: 'y',
+      type: NounType.Document,
+      subtype: 'note',
+      metadata: { v: 1 },
+      vector: VEC
+    })
+    // Pin right after BOTH adds — before the transact update — so X reads v1
+    // and Y still exists at this pin, unlike the live head after the rest of
+    // the workload runs.
+    const pinAfterBothAdds = brain.generation()
+    expect(pinAfterBothAdds).toBe(baseGen + 2) // ALSO pending — two un-flushed single-ops
+    expect(store.committedGeneration()).toBe(baseCommitted)
+
+    // A transact() flushes baseGen+1 and baseGen+2 first, then commits its
+    // own update as baseGen+3. If committed-vs-pending ordering ever broke,
+    // this is exactly the step that would land a commit ABOVE still-pending
+    // generations.
+    const db = await brain.transact([{ op: 'update', id: idX, metadata: { v: 3 } }])
+    await db.release()
+    expect(brain.generation()).toBe(baseGen + 3)
+    expect(store.committedGeneration()).toBe(baseGen + 3)
+
+    // A single-op delete, pending again (un-flushed).
+    await brain.remove(idY)
+    expect(brain.generation()).toBe(baseGen + 4)
+
+    // A point-in-time read pinned right after the two adds (before the
+    // transact update) must see X's PRE-update value and Y still present.
+    // This is precisely what resolveManyAt/resolveAt get WRONG if committed
+    // and pending generations were ever interleaved out of ascending order.
+    const past = await brain.asOf(pinAfterBothAdds)
+    const xAtPin = (await past.get(idX)) as any
+    expect(xAtPin?.metadata?.v).toBe(1)
+    const yAtPin = (await past.get(idY)) as any
+    expect(yAtPin?.metadata?.v).toBe(1) // not yet removed, as of this pin
+    await past.release()
+
+    // Live state reflects every later write, in the right order.
+    const xNow = (await brain.get(idX)) as any
+    expect(xNow.metadata.v).toBe(3)
+    expect(await brain.get(idY)).toBeNull()
+  })
+})

tests/unit/test-suite-coverage-guard.test.ts

@@ -4,7 +4,8 @@
  * config (so it never runs and gives false coverage confidence — the exact drift
  * that left ~27 test files un-run before 8.0). Every `*.test.ts` must either match
  * a gate config (`tests/unit/**`, `tests/integration/**`, `*.unit.test.ts`,
- * `*.integration.test.ts`) or be explicitly listed in MANUAL_ONLY below.
+ * `*.integration.test.ts`, or the perf lane's `tests/configs/vitest.perf.config.ts`
+ * — see PERF_LANE_FILES below) or be explicitly listed in MANUAL_ONLY below.
  */
 import { describe, it, expect } from 'vitest'
 import { readdirSync } from 'node:fs'
@@ -24,10 +25,12 @@ function allTestFiles(dir: string, out: string[] = []): string[] {
 }
 
 /**
- * Test files INTENTIONALLY excluded from the unit/integration gate: benchmarks,
- * scale/perf measurements, package-size checks, and real-model-load checks. They
- * are run manually (slow / need real resources), not in CI. Every entry is a
- * conscious decision — a NEW orphan not listed here fails the guard below.
+ * Test files INTENTIONALLY excluded from every automated gate — conformance
+ * suites invoked directly, and checks that need real resources (network,
+ * unusual scale) no CI lane provides. Wall-clock/scale benchmarks that DO
+ * run automatically belong to the perf lane (PERF_LANE_FILES / inGate
+ * below), not here. Every entry is a conscious decision — a NEW orphan not
+ * listed here fails the guard below.
  */
 const MANUAL_ONLY = new Set<string>([
   // Conformance suites run as an explicit gate stage (both engines run them
@@ -40,15 +43,11 @@ const MANUAL_ONLY = new Set<string>([
   // The sparse-store cut's shared operator rows (both engines run these):
   // explicit conformance-gate invocation, like its siblings.
   'tests/conformance/sparse-store-cut.test.ts',
-  'tests/api/performance-benchmarks.test.ts',
+  // NOT the perf lane: no wall-clock/scale assertion, so it does not belong
+  // in tests/configs/vitest.perf.config.ts's include list — genuinely run
+  // by hand only.
   'tests/critical-neural-validation.test.ts',
-  'tests/critical-performance-benchmark.test.ts',
-  'tests/model-loading.test.ts',
   'tests/package-size-breakdown.test.ts',
-  'tests/package-size-limit.test.ts',
-  'tests/performance/graph-scale-performance.test.ts',
-  'tests/performance/triple-intelligence-scale.test.ts',
-  'tests/performance/typeAware.bench.test.ts',
   // Cross-engine field-addressing conformance suite: pinned bit-for-bit against
   // the native accelerator's implementation of the SAME contract, and invoked
   // directly (`npx vitest run tests/conformance/namespace-law.test.ts`), never
@@ -59,6 +58,21 @@ const MANUAL_ONLY = new Set<string>([
   'tests/conformance/namespace-law.test.ts'
 ])
 
+/**
+ * The perf lane's own gate: `tests/configs/vitest.perf.config.ts`, run by
+ * `npm run test:perf`. Mirrors that config's `include` list — kept in sync
+ * by inspection, the same convention that config uses against the root
+ * gate's exclude list (see its own header comment). A file that runs here
+ * is GATED, not manual: it belongs in this set (or the `tests/performance/`
+ * prefix below), never in MANUAL_ONLY.
+ */
+const PERF_LANE_FILES = new Set<string>([
+  'tests/critical-performance-benchmark.test.ts',
+  'tests/api/performance-benchmarks.test.ts',
+  'tests/package-size-limit.test.ts',
+  'tests/model-loading.test.ts'
+])
+
 function inGate(rel: string): boolean {
   return (
     rel.startsWith('tests/unit/') ||
@@ -67,7 +81,11 @@ function inGate(rel: string): boolean {
     // ('tests/lifecycle/**/*.test.ts'; see tests/lifecycle/README.md).
     rel.startsWith('tests/lifecycle/') ||
     rel.endsWith('.unit.test.ts') ||
-    rel.endsWith('.integration.test.ts')
+    rel.endsWith('.integration.test.ts') ||
+    // The perf lane (see PERF_LANE_FILES above) — mirrors
+    // tests/configs/vitest.perf.config.ts's `tests/performance/**` glob.
+    rel.startsWith('tests/performance/') ||
+    PERF_LANE_FILES.has(rel)
   )
 }
 

tests/vfs/vfs-search-path-scope.unit.test.ts

@@ -0,0 +1,165 @@
+/**
+ * @module tests/vfs/vfs-search-path-scope.unit
+ * @description `vfs.search({ path })` scopes with a SERVED filter.
+ *
+ * The scope used to be emitted as `path: { $startsWith }` — an operator that is
+ * not in the filter vocabulary at all, and whose `$`-less spelling the metadata
+ * index refuses by the served-operator law (an equality/range posting index
+ * cannot evaluate a substring without reading every row). Every path-scoped VFS
+ * search threw; none has ever worked on this engine line.
+ *
+ * The scope is now a half-open range over `metadata.path`, which is the VFS's
+ * truth, is indexed on every VFS entity, and is served by the ordered range
+ * operators: `[dir + '/', dir + '0')` — '0' being the code point after '/', so
+ * membership in the range is EXACTLY "carries the prefix `dir/`". The
+ * non-recursive scope is the directory's own identity, `parent`, an equality.
+ *
+ * These pins hold the answer (descendants at every depth, siblings never — the
+ * `/scope-sibling` trap included), the shape (the operators the search emits
+ * are answered by the index's own door, never refused), and the law that the
+ * scope narrows the search BEFORE it runs rather than filtering an over-fetch.
+ */
+import { describe, it, expect, beforeAll, afterAll, vi } from 'vitest'
+import { VirtualFileSystem } from '../../src/vfs/VirtualFileSystem.js'
+import { Brainy } from '../../src/brainy.js'
+import { VFSErrorCode } from '../../src/vfs/types.js'
+
+/** A word every fixture file carries, so the text leg reaches all of them. */
+const TOKEN = 'quasar'
+
+describe('vfs.search({ path }) scopes with a served filter', () => {
+  let brain: Brainy
+  let vfs: VirtualFileSystem
+
+  /** In scope for '/scope', at three depths. */
+  const inScope = ['/scope/a.txt', '/scope/sub/b.txt', '/scope/sub/deep/c.txt']
+  /** Out of scope — including the two prefix traps a naive test misses. */
+  const outOfScope = ['/scope-sibling/d.txt', '/scope0/e.txt', '/elsewhere/f.txt', '/g.txt']
+
+  beforeAll(async () => {
+    brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' }, silent: true })
+    await brain.init()
+    vfs = brain.vfs
+    await vfs.init()
+
+    await vfs.mkdir('/scope/sub/deep', { recursive: true })
+    await vfs.mkdir('/scope-sibling', { recursive: true })
+    await vfs.mkdir('/scope0', { recursive: true })
+    await vfs.mkdir('/elsewhere', { recursive: true })
+
+    for (const path of [...inScope, ...outOfScope]) {
+      await vfs.writeFile(path, `${TOKEN} content for ${path}`)
+    }
+  })
+
+  afterAll(async () => {
+    await vfs?.close()
+    await brain?.close()
+  })
+
+  it('includes every descendant depth and excludes every sibling', async () => {
+    const results = await vfs.search(TOKEN, { path: '/scope', limit: 50 })
+    const paths = results.map((r) => r.path).sort()
+
+    expect(paths).toEqual([...inScope].sort())
+    for (const path of outOfScope) expect(paths).not.toContain(path)
+  })
+
+  it('a trailing slash and a doubled slash name the same scope', async () => {
+    const plain = await vfs.search(TOKEN, { path: '/scope', limit: 50 })
+    const trailing = await vfs.search(TOKEN, { path: '/scope/', limit: 50 })
+    const doubled = await vfs.search(TOKEN, { path: '//scope//', limit: 50 })
+
+    const ids = (rs: Array<{ entityId: string }>) => rs.map((r) => r.entityId).sort()
+    expect(ids(trailing)).toEqual(ids(plain))
+    expect(ids(doubled)).toEqual(ids(plain))
+  })
+
+  it('the root scope is every VFS file — it adds no clause to narrow with', async () => {
+    const rooted = await vfs.search(TOKEN, { path: '/', limit: 50 })
+    const unscoped = await vfs.search(TOKEN, { limit: 50 })
+
+    const paths = rooted.map((r) => r.path).sort()
+    expect(paths).toEqual([...inScope, ...outOfScope].sort())
+    expect(paths).toEqual(unscoped.map((r) => r.path).sort())
+  })
+
+  it('recursive: false is the immediate children, not the subtree', async () => {
+    const results = await vfs.search(TOKEN, { path: '/scope', recursive: false, limit: 50 })
+    expect(results.map((r) => r.path)).toEqual(['/scope/a.txt'])
+  })
+
+  it('recursive: false on a path that does not exist refuses by name', async () => {
+    await expect(
+      vfs.search(TOKEN, { path: '/no-such-dir', recursive: false, limit: 50 })
+    ).rejects.toMatchObject({ code: VFSErrorCode.ENOENT })
+  })
+
+  it('every operator the search emits is ANSWERED by the index door, never refused', async () => {
+    const index = (brain as any).metadataIndex
+    const emitted: any[] = []
+    const find = vi.spyOn(brain as any, 'find')
+    try {
+      await vfs.search(TOKEN, { path: '/scope', limit: 50 })
+      await vfs.search(TOKEN, { path: '/scope/sub', where: { mimeType: 'text/plain' }, limit: 50 })
+      await vfs.search(TOKEN, { path: '/scope', recursive: false, limit: 50 })
+      await vfs.search(TOKEN, { path: '/', limit: 50 })
+      for (const call of find.mock.calls) emitted.push((call[0] as any).where)
+    } finally {
+      find.mockRestore()
+    }
+
+    expect(emitted).toHaveLength(4)
+    for (const where of emitted) {
+      // The door itself is the judge: an operator outside the served set is
+      // REFUSED here (BrainyError INVALID_QUERY), never answered.
+      await expect(index.getIdsForFilter(where)).resolves.toBeInstanceOf(Array)
+    }
+
+    // And the scope really is a range on the path — the shape this fix chose.
+    expect(emitted[0].path).toEqual({ gte: '/scope/', lt: '/scope0' })
+    expect(emitted[3].path).toBeUndefined()
+  })
+
+  it('the scope narrows the search before it runs — no over-fetch to filter', async () => {
+    const index = (brain as any).metadataIndex
+    const filter = vi.spyOn(index, 'getIdsForFilter')
+    let universe: string[] = []
+    try {
+      await vfs.search(TOKEN, { path: '/scope', limit: 50 })
+      // The search's own call — the one carrying the scope. (Path resolution
+      // asks this same door for the root, before the search is built.)
+      const scoped = filter.mock.calls.findIndex(
+        (c) => (c[0] as any)?.path?.gte === '/scope/'
+      )
+      expect(scoped).toBeGreaterThanOrEqual(0)
+      universe = (await filter.mock.results[scoped].value) as string[]
+    } finally {
+      filter.mockRestore()
+    }
+
+    // The id universe the index resolved for the search is already the scope:
+    // three files, and not one row from outside it.
+    const rows = await brain.batchGet(universe)
+    const paths = [...rows.values()].map((e: any) => e.metadata.path).sort()
+    expect(paths).toEqual([...inScope].sort())
+  })
+
+  it('the range answers the same ids as walking the tree', async () => {
+    // The path is the truth and the Contains edges are its projection; a scope
+    // read from the truth must agree with one walked over the projection.
+    const walked: string[] = []
+    const walk = async (dir: string): Promise<void> => {
+      for (const name of await vfs.readdir(dir)) {
+        const child = dir === '/' ? `/${name}` : `${dir}/${name}`
+        const stat = await vfs.stat(child)
+        if (stat.isDirectory()) await walk(child)
+        else walked.push(child)
+      }
+    }
+    await walk('/scope')
+
+    const searched = await vfs.search(TOKEN, { path: '/scope', limit: 50 })
+    expect(searched.map((r) => r.path).sort()).toEqual(walked.sort())
+  })
+})

vitest.config.ts

@@ -2,9 +2,16 @@ import { defineConfig } from 'vitest/config'
 
 /**
  * Vitest Configuration - Optimized for Memory-Intensive Tests
- * 
+ *
  * Handles ONNX transformer model testing (4-8GB memory requirement)
  * Based on 2024-2025 best practices
+ *
+ * THE CORRECTNESS GATE: this is the config a bare `vitest run` (no
+ * `--config` flag) picks up — the delta gate and CI both invoke it that
+ * way. See CONTRIBUTING.md's "Test gate" section for the full picture.
+ * Wall-clock/scale benchmarks and tests whose outcome depends on the host
+ * machine or network rather than the code are excluded below and run on
+ * demand instead, in their own slot: `npm run test:perf`.
  */
 export default defineConfig({
   test: {
@@ -38,7 +45,29 @@ export default defineConfig({
       'node_modules/**',
       'dist/**',
       'scripts/**',
-      '**/*.browser.test.ts'
+      '**/*.browser.test.ts',
+
+      // Wall-clock/scale benchmark family — timing assertions and scale
+      // sweeps whose pass/fail depends on the host machine's speed, not on
+      // the code. Whole files only (a file that mixes correctness describes
+      // with a perf describe stays in the gate). Run on demand via
+      // `npm run test:perf`, which targets exactly this list.
+      'tests/performance/**',
+      'tests/critical-performance-benchmark.test.ts',
+      'tests/api/performance-benchmarks.test.ts',
+
+      // Environment-dependent by construction, not timing-based:
+      // package-size-limit shells out to the `npm` CLI (not guaranteed
+      // present — the functional gate lane is Bun-only host-mode with no
+      // Node.js runtime) and parses npm-version-specific `npm pack` notice
+      // text; model-loading's "Real Model Download Integration" case makes
+      // a genuine, unmocked network call to HuggingFace (its own header
+      // says "Uses REAL transformer models - NO MOCKING"), and the whole
+      // file imports `../src/embeddings/model-manager.js`, which no longer
+      // exists anywhere under src/ — neither belongs in a gate that must be
+      // deterministic.
+      'tests/package-size-limit.test.ts',
+      'tests/model-loading.test.ts'
     ],
     
     // REPORTERS: Dot for CI, verbose for local