docs(releases): the 11.0.5 note — graph-first finds in production, bounded recovery

The fleet's releases wall reads one public URL per product. These files are
that door for Brainy and Open Brainy: newest first, honest history from the
changelog, one entry appended by every release from here on.

CHANGELOG.md

@@ -2,18 +2,6 @@
 
 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.
 
-### [10.4.6](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)

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "@soulcraftlabs/brainy",
-  "version": "10.4.6",
+  "version": "10.4.4",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "@soulcraftlabs/brainy",
-      "version": "10.4.6",
+      "version": "10.4.4",
       "license": "MIT",
       "dependencies": {
         "@msgpack/msgpack": "^3.1.2",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@soulcraftlabs/brainy",
-  "version": "10.4.6",
+  "version": "10.4.4",
   "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",

releases/brainy.json

@@ -0,0 +1,76 @@
+{
+  "product": "brainy",
+  "entries": [
+    {
+      "version": "11.0.5",
+      "date": "2026-09-02",
+      "headline": "Graph-first finds in production, and opens that stop rescanning history",
+      "items": [
+        "find({ connected, where }) now walks the neighbours first and filters only those rows through a native door — correct at every page and O(neighbours), never the whole store.",
+        "related() with a list of verb types returns every requested kind (a fast path had silently kept only the first).",
+        "Deferred-embedding recovery resumes from a low-water mark instead of rescanning the whole generation log at every open — measured at two minutes on a large brain, now milliseconds."
+      ],
+      "url": null,
+      "thumb": null
+    },
+    {
+      "version": "11.0.4",
+      "date": "2026-09-01",
+      "headline": "Closes in milliseconds, index rebuilds without the disk-sync storm",
+      "items": [
+        "close() no longer pays deferred compaction or waits out an in-flight rebuild — measured 8 ms against the 4-minute closes it replaces; deferred work resumes at the next open, in the background.",
+        "The metadata index's rebuild syncs to disk per shard instead of per row, and the durability point moved to the publish step — the same guarantee, a fraction of the disk traffic.",
+        "A new native filter door evaluates queries over exactly the candidate rows a graph walk found, never the whole store."
+      ],
+      "url": null,
+      "thumb": null
+    },
+    {
+      "version": "11.0.3",
+      "date": "2026-09-01",
+      "headline": "The embedding upgrade ceremony runs on every brain",
+      "items": [
+        "A brain opened through the standard plugin now carries its embedding-model identity, so the full-precision upgrade ceremony can run on it.",
+        "A one-fix release; nothing else changed."
+      ],
+      "url": null,
+      "thumb": null
+    },
+    {
+      "version": "11.0.2",
+      "date": "2026-08-31",
+      "headline": "One embedding quality everywhere, 3–4× faster imports",
+      "items": [
+        "Every runtime embeds with the same full-precision model — search quality no longer depends on where you run.",
+        "Bulk embedding measured 3.1–4.2× faster, and an online re-embed ceremony upgrades existing stores without downtime.",
+        "The engine's change feed is documented, with the SSE/WebSocket fan-out pattern for realtime surfaces."
+      ],
+      "url": null,
+      "thumb": null
+    },
+    {
+      "version": "11.0.1",
+      "date": "2026-08-31",
+      "headline": "Deletes inside transactions are safe",
+      "items": [
+        "Deleting relations inside a transact() no longer corrupts index bookkeeping.",
+        "A store that deletes its last relation keeps serving instead of refusing."
+      ],
+      "url": null,
+      "thumb": null
+    },
+    {
+      "version": "11.0.0",
+      "date": "2026-08-28",
+      "headline": "One install, one engine — Brainy",
+      "items": [
+        "The former two-package pair is one package: the native engine under the familiar API. One import is the whole install.",
+        "A missing native build refuses loudly with its cures named; nothing falls back silently.",
+        "Stores open in place — no migration."
+      ],
+      "url": null,
+      "thumb": null
+    }
+  ],
+  "history": "The version line continues from the 4.3.x native-engine releases; their record lives in the product repository's CHANGELOG.md."
+}

releases/open-brainy.json

@@ -0,0 +1,110 @@
+{
+  "product": "open-brainy",
+  "entries": [
+    {
+      "version": "10.4.9",
+      "date": "2026-09-02",
+      "headline": "Graph-first finds, honest verb arrays, and opens that stop rescanning history",
+      "items": [
+        "find({ connected, where }) now walks the neighbours first and filters only those rows — correct at every page, and O(neighbours) instead of O(store).",
+        "related() with a list of verb types (or sources, or targets) returns every requested kind — four fast paths silently kept only the first.",
+        "Deferred-embedding recovery resumes from a low-water mark instead of rescanning the whole generation log at every open — measured at two minutes on a large brain, now milliseconds."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.9",
+      "thumb": null
+    },
+    {
+      "version": "10.4.7",
+      "date": "2026-09-01",
+      "headline": "Count ledgers can no longer race themselves",
+      "items": [
+        "Concurrent count flushes coalesce into one writer with a trailing pass — parallel flushes can no longer corrupt a store's count ledger.",
+        "Atomic writes carry a per-process sequence, so two processes' temp files can never collide."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.7",
+      "thumb": null
+    },
+    {
+      "version": "10.4.6",
+      "date": "2026-08-31",
+      "headline": "Transactions cross the index seam safely",
+      "items": [
+        "Deleting relations inside a transact() no longer fails against the metadata index — operations take a JSON-safe view at the moment they execute.",
+        "Fixes a class of transaction failures on stores with integer-mapped relation endpoints."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.6",
+      "thumb": null
+    },
+    {
+      "version": "10.4.5",
+      "date": "2026-08-31",
+      "headline": "Recovery tells the truth, docs live at home",
+      "items": [
+        "A torn generation-log tail is a terminal verdict with a named cure — never an endless wait at open.",
+        "A sealed segment declares only the generations it actually holds.",
+        "The engine's documentation now publishes from its own repository."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.5",
+      "thumb": null
+    },
+    {
+      "version": "10.4.4",
+      "date": "2026-08-28",
+      "headline": "Faster opens, quieter idle",
+      "items": [
+        "Opening a store discovers generations from directory names instead of walking the log, and answers \"any entities?\" with one directory read.",
+        "The flush-request watch is event-driven; idle stores stop paying a polling heartbeat.",
+        "A slow open now names the exact step it is in, so operators see what is being paid and why."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.4",
+      "thumb": null
+    },
+    {
+      "version": "10.4.3",
+      "date": "2026-08-27",
+      "headline": "Open Brainy, under its own name",
+      "items": [
+        "The same engine as 10.4.2, now published as @soulcraftlabs/brainy — the MIT reference engine, on The Source.",
+        "No code changes; your imports change once and everything else stays put."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.3",
+      "thumb": null
+    },
+    {
+      "version": "10.4.2",
+      "date": "2026-08-27",
+      "headline": "Vectors that lie are refused, counts that drift are caught",
+      "items": [
+        "A zero-norm vector is not a vector: the index refuses them, rebuilds skip them, and a sanctioned unvector door removes them cleanly.",
+        "The canonical count ledger derives from identity records and marks legacy-derived ledgers suspect at load.",
+        "Plugin activation failures keep their original error as cause, so the real frame reaches your logs."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.2",
+      "thumb": null
+    },
+    {
+      "version": "10.4.1",
+      "date": "2026-08-26",
+      "headline": "Writes that change nothing cost nothing",
+      "items": [
+        "The read gate is per index family, and a write carrying unchanged data never re-embeds.",
+        "The vectored-row count joins the ledger, so vector coverage is a number you can read, not a guess."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.1",
+      "thumb": null
+    },
+    {
+      "version": "10.4.0",
+      "date": "2026-08-26",
+      "headline": "Repair routing, the vector ledger, and honest empties",
+      "items": [
+        "Repairs route to the index that owns the damage, and the open gate closes the vector leg until coverage is proven.",
+        "An empty string is real data, not a missing field.",
+        "The metadata crossing never carries raw integer relation endpoints — a whole class of serialization faults closed."
+      ],
+      "url": "https://source.soulcraft.com/soulcraftlabs/open-brainy/releases/tag/v10.4.0",
+      "thumb": null
+    }
+  ],
+  "history": "Earlier releases are recorded in CHANGELOG.md in this repository."
+}

scripts/release.sh

@@ -237,7 +237,7 @@ fi
 # and RELEASES.md are the record; this just gives The Source's UI a release page).
 echo -e "${BLUE}🔟 Creating release page on The Source...${NC}"
 if [ -n "${FORGEJO_RELEASE_TOKEN:-}" ]; then
-  if curl -sf -X POST "https://source.soulcraft.com/api/v1/repos/soulcraft/brainy/releases" \
+  if curl -sf -X POST "https://source.soulcraft.com/api/v1/repos/soulcraftlabs/open-brainy/releases" \
     -H "Authorization: token ${FORGEJO_RELEASE_TOKEN}" -H "Content-Type: application/json" \
     -d "{\"tag_name\":\"v${NEW_VERSION}\",\"name\":\"v${NEW_VERSION}\",\"prerelease\":${PRERELEASE}}" >/dev/null; then
     echo -e "${GREEN}✅ Release page created on The Source${NC}\n"

src/brainy.ts

@@ -15,7 +15,6 @@ import { JsHnswVectorIndex } from './hnsw/hnswIndex.js'
 import { createStorage, resolveFilesystemRoot } from './storage/storageFactory.js'
 import type { StorageOptions } from './storage/storageFactory.js'
 import { rebuildCounts } from './utils/rebuildCounts.js'
-import { jsonSafeIndexMetadata } from './utils/jsonSafeIndexMetadata.js'
 import type { MetadataWriteBuffer } from './utils/metadataWriteBuffer.js'
 import { BaseStorage } from './storage/baseStorage.js'
 import {
@@ -1820,31 +1819,31 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       // a deferred write's ack and its background embed DELAYED a vector;
       // this is where it lands.
       if (!this.isReadOnly) {
-        // BEHIND THE DOORS (the open pays nothing here): the bridge + the
-        // recovery fold run as one latched background task; the embed worker
-        // starts when it settles. A pending embed's outcome was always
-        // eventual — moving its recovery off the open's foreground changes
-        // when the worker starts, never whether a marker is honored.
-        // awaitPendingEmbeds() and close() wait on the latch first.
-        this._pendingEmbedRecovery = (async () => {
-          try {
-            await this.bridgeLegacyPendingEmbedSidecars()
-            await this.recoverPendingEmbedsFromLog()
-            if (this._pendingEmbedIds.size > 0) {
-              prodLog.info(
-                `[Brainy] ${this._pendingEmbedIds.size} deferred embed(s) pending from a previous ` +
-                  `session — resuming in the background`
-              )
-              const t = setTimeout(() => this.kickEmbedWorker(), 0)
-              ;(t as { unref?: () => void }).unref?.()
-            }
-          } catch (err) {
-            prodLog.warn(
-              `[Brainy] pending-embed recovery failed: ${(err as Error).message} — ` +
-                `the log's markers remain durable; recovery retries next open`
+        try {
+          await step(
+            'bridge-pending-embed-sidecars',
+            'migrating any pre-log deferred-embed marker files into the generation log',
+            () => this.bridgeLegacyPendingEmbedSidecars()
+          )
+          await step(
+            'recover-pending-embeds',
+            'folding the generation log\'s deferred-embed markers back into the pending set',
+            () => this.recoverPendingEmbedsFromLog()
+          )
+          if (this._pendingEmbedIds.size > 0) {
+            prodLog.info(
+              `[Brainy] ${this._pendingEmbedIds.size} deferred embed(s) pending from a previous ` +
+                `session — resuming in the background`
             )
+            const t = setTimeout(() => this.kickEmbedWorker(), 0)
+            ;(t as { unref?: () => void }).unref?.()
           }
-        })()
+        } catch (err) {
+          prodLog.warn(
+            `[Brainy] pending-embed recovery failed: ${(err as Error).message} — ` +
+              `the log's markers remain durable; recovery retries next open`
+          )
+        }
       }
 
       // PHASE 4 of 5 — "VFS bootstrap": shutdown-hook registration, blob
@@ -2408,19 +2407,6 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    */
   private static readonly PENDING_EMBED_PREFIX = '_system/pending_embeds/'
 
-  /**
-   * Storage-root-relative path of the ADVISORY pending-embed low-water mark:
-   * `{ generation, writtenAt }`, written whenever the pending set drains to
-   * empty (and at clean close when empty). Every marker in facts at or below
-   * `generation` is consumed, so recovery scans from `generation + 1`. The
-   * mark is advisory and monotone-safe: stale-low costs a longer scan, never
-   * a lost marker; it is never required for correctness.
-   */
-  private static readonly PENDING_EMBED_LOWWATER_PATH = '_system/pending_embeds_lowwater.json'
-
-  /** Resolves when the background pending-embed recovery fold has settled (open arms it). */
-  private _pendingEmbedRecovery: Promise<void> | null = null
-
   /**
    * @description Mark a deferred embed pending (MT5): the id joins the
    * in-memory fast-path set and the returned `embed.pending` record is
@@ -2448,40 +2434,6 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    */
   private clearPendingEmbed(id: string): void {
     this._pendingEmbedIds.delete(id)
-    if (this._pendingEmbedIds.size === 0) this.maybeWriteEmbedLowWater()
-  }
-
-  /**
-   * @description Advance the advisory low-water mark: called at drain-to-empty
-   * (and at clean close when empty), it records the fact log's CURRENT head —
-   * with the set empty, every marker at or below the head has been consumed,
-   * so the next open's recovery fold scans only what comes after. Fire-and-
-   * forget at the drain (close() awaits the core); loud on failure: a missed
-   * write costs the next open a longer scan, never a marker. No-op without a
-   * fact log (no durable markers exist there) and on read-only opens.
-   */
-  private maybeWriteEmbedLowWater(): void {
-    void this.writeEmbedLowWater()
-  }
-
-  /** The awaitable core of {@link maybeWriteEmbedLowWater} — close() awaits it. */
-  private async writeEmbedLowWater(): Promise<void> {
-    if (this.isReadOnly) return
-    const log = this.generationStore ? this.generationStore.getFactLog() : null
-    if (!log) return
-    const generation = log.headGeneration()
-    if (!(generation > 0)) return
-    try {
-      await this.storage.writeRawObject(Brainy.PENDING_EMBED_LOWWATER_PATH, {
-        generation,
-        writtenAt: Date.now()
-      })
-    } catch (err) {
-      prodLog.warn(
-        `[Brainy] pending-embed low-water write failed at generation ${generation}: ` +
-          `${(err as Error).message} — the next open scans from the previous mark`
-      )
-    }
   }
 
   /**
@@ -2492,14 +2444,9 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    * survives the fold is exactly the set of acknowledged deferred writes
    * whose vectors have not landed.
    *
-   * BOUND: the scan starts at the advisory low-water mark
-   * ({@link Brainy.PENDING_EMBED_LOWWATER_PATH}) — the log head at which the
-   * pending set last drained to empty — so a settled brain reads only the
-   * facts since then, not its whole history. Without a mark (first open
-   * after upgrade) it scans from generation 1, once; a stale-low mark costs
-   * a longer scan, never a marker. The fold runs BEHIND the doors (open
-   * arms it as a background task and the embed worker starts when it
-   * settles); {@link awaitPendingEmbeds} and close() wait for it first.
+   * BOUND (honest): no durable low-water mark exists for the earliest
+   * unconsumed pending, so the fold scans the log's committed facts from
+   * generation 1 — a sequential read of the log at open, O(log bytes).
    * It is SKIPPED WHOLESALE when the log has never had a v2 tail
    * ({@link FactLog.hasV2History} — v1 facts cannot carry marker records),
    * so pre-cutover brains pay nothing; on a mixed log the scan still reads
@@ -2512,18 +2459,7 @@ export class Brainy<T = any> implements BrainyInterface<T> {
   private async recoverPendingEmbedsFromLog(): Promise<void> {
     const log = this.generationStore.getFactLog()
     if (!log || !log.hasV2History()) return
-    let fromGeneration = 1
-    try {
-      const mark = (await this.storage.readRawObject(Brainy.PENDING_EMBED_LOWWATER_PATH)) as {
-        generation?: number
-      } | null
-      if (mark && typeof mark.generation === 'number' && mark.generation > 0) {
-        fromGeneration = mark.generation + 1
-      }
-    } catch {
-      // No mark (or unreadable): scan from 1 — correctness over cost.
-    }
-    const scan = log.scanFacts({ fromGeneration })
+    const scan = log.scanFacts({ fromGeneration: 1 })
     for await (const batch of scan.batches()) {
       for (const fact of batch.facts) {
         for (const record of fact.records ?? []) {
@@ -2710,7 +2646,6 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    * before I proceed" callers use this; nothing else ever needs to wait.
    */
   public async awaitPendingEmbeds(): Promise<void> {
-    if (this._pendingEmbedRecovery) await this._pendingEmbedRecovery
     while (this._pendingEmbedIds.size > 0 || this._embedWorkerFlight) {
       this.kickEmbedWorker()
       await (this._embedWorkerFlight ?? Promise.resolve())
@@ -4268,19 +4203,32 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    */
   /**
    * @description A JSON-safe view of a record bound for the metadata-index
-   * crossing — delegates to the shared {@link jsonSafeIndexMetadata} leaf,
-   * which the metadata-index transaction operations ALSO apply at execute
-   * and rollback time. This plan-time wrap alone proved insufficient: it
-   * returns the same reference when the record is clean, and `transact()`'s
-   * delete legs share that reference with a graph-retraction op whose
-   * execute-time endpoint resolution mirrors BigInt ints onto it (the full
-   * aliasing story lives on the leaf module's doc).
+   * crossing. The seam's metadata is JSON-safe BY CONTRACT (a native provider
+   * serializes it; u64 ints as Number corrupt above 2^53) — but
+   * {@link resolveVerbEndpointInts} MIRRORS the resolved endpoint ints onto
+   * the verb object itself as BigInt (`verb.sourceInt`/`targetInt`), so a
+   * verb object reused as index metadata carried BigInts into
+   * JSON.stringify, which throws, aborting the whole transaction (found by
+   * the first joint pair gate). 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.
    * @param metadata - The candidate index-metadata record.
    * @returns The same object when already JSON-safe, else a shallow copy
    *   without the BigInt-valued keys.
    */
   private static jsonSafeIndexMetadata(metadata: unknown): unknown {
-    return jsonSafeIndexMetadata(metadata)
+    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
   }
 
   private metadataIndexRetractionOp(
@@ -7344,47 +7292,6 @@ export class Brainy<T = any> implements BrainyInterface<T> {
         await this.verifyMetadataLive()
       }
 
-      // PLANNED FIND (optional provider door, `MetadataIndexProvider.planFindPage`).
-      //
-      // The stage doors below 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 and materializes ids only for the page.
-      //
-      // The hook sits ABOVE the branch selection because the branches are what
-      // decide stage order per call site; an index that plans has to be asked
-      // before that choice is made, not inside one of its arms.
-      //
-      // Optional and additive: a provider without the door, and any shape the
-      // door hands back, take exactly the path they always took. `null` is a
-      // routing decision the door must make BEFORE doing any work — never a
-      // partial answer. Every guard above still ran (readiness, the migration
-      // gate, the where-clause validation, the metadata cold-read guard), and
-      // the serving law is applied here on the way out: an empty answer is
-      // re-verified against the index that produced it before it is believed.
-      const planningIndex = this.metadataIndex as unknown as MetadataIndexProvider
-      if (typeof planningIndex.planFindPage === 'function') {
-        const planned = await planningIndex.planFindPage(params, [...hiddenIds], this.graphIndex)
-        if (planned !== null && planned !== undefined) {
-          if (planned.ids.length === 0) {
-            // A cold adjacency can report a size yet hold no edges, so an empty
-            // graph answer is not truth until the adjacency verifies live. A
-            // genuinely edgeless anchor verifies and the empty result stands.
-            if (planned.emptyAt === 'graph') await this.verifyGraphAdjacencyLive()
-            return []
-          }
-          const plannedEntities = await this.batchGet(planned.ids)
-          const plannedResults: Result<T>[] = []
-          for (const id of planned.ids) {
-            const entity = plannedEntities.get(id)
-            if (entity) plannedResults.push(this.createResult(id, 1.0, entity))
-          }
-          return plannedResults
-        }
-      }
-
       // Handle metadata-only queries (no vector search needed)
       if (!hasVectorSearchCriteria && !hasGraphCriteria && hasFilterCriteria) {
         // Build filter for metadata index
@@ -7575,37 +7482,7 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       // JS path — there the materialized `candidateIds` restricts the walk instead.
       let preResolvedAllowedIds: OpaqueIdSet | undefined
 
-      // Graph-first law (10.4.8, BRAINY-PROD-LATENCY-TRIAD rounds 44/45): with
-      // `connected` present the NEIGHBOUR SET is the candidate universe. It is
-      // resolved first from the adjacency (O(neighbours)), the metadata filter
-      // is evaluated over those ids only, and paging happens LAST. The earlier
-      // order materialized the whole-store filtered id list, paged it, hydrated
-      // the page, and only then intersected with the neighbours — O(store) per
-      // call, and a neighbour outside the first page was silently dropped.
-      let graphFirstIds: string[] | null = null
-      if (hasGraphCriteria) {
-        graphFirstIds = await this.resolveConnectedIds(params)
-        if (hiddenIds.size > 0) {
-          graphFirstIds = graphFirstIds.filter((id) => !hiddenIds.has(id))
-        }
-        if (
-          graphFirstIds.length > 0 &&
-          (params.where || params.type || params.subtype || params.service || params.excludeVFS)
-        ) {
-          preResolvedFilter = this.buildMetadataFilter(params)
-          graphFirstIds = await this.filterIdsWithinBelted(preResolvedFilter, graphFirstIds)
-        }
-        if (graphFirstIds.length === 0) {
-          return []
-        }
-        if (!hasVectorSearchCriteria) {
-          return await this.pageConnectedIds(params, graphFirstIds)
-        }
-        // The vector leg walks ONLY the neighbours (its candidate walk). The
-        // filter is already applied above, so no opaque universe is produced —
-        // it would describe the whole store, not the neighbour set.
-        preResolvedMetadataIds = graphFirstIds
-      } else if (params.where || params.type || params.subtype || params.service || params.excludeVFS) {
+      if (params.where || params.type || params.subtype || params.service || params.excludeVFS) {
         preResolvedFilter = this.buildMetadataFilter(params)
         preResolvedMetadataIds = await this.filterIdsBelted(preResolvedFilter)
 
@@ -7794,11 +7671,9 @@ export class Brainy<T = any> implements BrainyInterface<T> {
         }
       }
 
-      // The text leg of a hybrid find has no candidate door, so its hits are
-      // held to the neighbour set here; the vector leg walked only the neighbours.
-      if (graphFirstIds !== null && results.length > 0) {
-        const neighbourSet = new Set(graphFirstIds)
-        results = results.filter((r) => neighbourSet.has(r.id))
+      // Graph search component with O(1) traversal
+      if (params.connected) {
+        results = await this.executeGraphSearch(params, results)
       }
 
       // Apply fusion scoring if requested
@@ -12913,29 +12788,6 @@ export class Brainy<T = any> implements BrainyInterface<T> {
     }
   }
 
-  /**
-   * The id-scoped twin of {@link filterIdsBelted}: evaluate `filter` over `ids`
-   * only, through the provider's own evaluation so the answer can never drift
-   * from `getIdsForFilter`'s. A provider without the door is served by its
-   * whole-store answer intersected here (the reference index implements the
-   * door itself). Same belt: field refusals cross as `BrainyFieldRefusal`.
-   */
-  private async filterIdsWithinBelted(filter: unknown, ids: readonly string[]): Promise<string[]> {
-    this.ensureIndexesLoaded(['metadata'])
-    const mip = this.metadataIndex as unknown as MetadataIndexProvider
-    try {
-      if (typeof mip.filterIdsWithin === 'function') {
-        return await mip.filterIdsWithin(filter, ids)
-      }
-      const matched = new Set(await this.metadataIndex.getIdsForFilter(filter))
-      return ids.filter((id) => matched.has(id))
-    } catch (err) {
-      const normalized = asBrainyFieldRefusal(err)
-      if (normalized) throw normalized
-      throw err
-    }
-  }
-
   async getIndexStatus(): Promise<{
     initialized: boolean
     /** `true` once open()'s index-build-if-needed step has run. Named for API
@@ -15919,16 +15771,16 @@ export class Brainy<T = any> implements BrainyInterface<T> {
   }
   
   /**
-   * Resolve `params.connected` to the neighbour id set — the graph-first
-   * find's candidate universe (deterministic traversal order, anchors excluded).
+   * Execute graph search component.
    *
    * Honors the full `GraphConstraints` contract: multi-hop `depth` (breadth-first via
-   * `neighbors()`), `via`/`type` verb-type filtering, and `direction`. An empty set
-   * is re-verified against the adjacency before it is believed — a not-serving
-   * adjacency throws rather than answering `[]` as truth.
+   * `neighbors()`), `via`/`type` verb-type filtering, and `direction`. Previously this read
+   * only `from`/`to`/`direction` and did a single 1-hop `getNeighbors()`, so `depth` and `via`
+   * were silently ignored — `find({ connected: { from, depth: 3 } })` returned only the
+   * immediate neighbour at every depth.
    */
-  private async resolveConnectedIds(params: FindParams<T>): Promise<string[]> {
-    if (!params.connected) return []
+  private async executeGraphSearch(params: FindParams<T>, existingResults: Result<T>[]): Promise<Result<T>[]> {
+    if (!params.connected) return existingResults
 
     const { from, to, depth, direction = 'both' } = params.connected
     const via = params.connected.via ?? params.connected.type
@@ -15982,8 +15834,8 @@ export class Brainy<T = any> implements BrainyInterface<T> {
           if (anchorInt === undefined) return new Set() // unmapped → no relations
 
           const verbTypeIndex = TypeUtils.getVerbIndex(via as VerbType)
-          // No limit: match the JS BFS exactly — the page is cut downstream,
-          // after the metadata filter, by pageConnectedIds / the candidate walk.
+          // No limit: match the JS BFS exactly — overall result limiting happens
+          // downstream against existingResults.
           const reachedInts = await provider.findConnectedSubtype(
             anchorInt, verbTypeIndex, subtypeArr[0], effectiveDepth, null
           )
@@ -16068,44 +15920,22 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       await this.verifyGraphAdjacencyLive()
     }
 
-    return [...connectedIds]
-  }
-
-  /**
-   * Page and hydrate an already-filtered neighbour set — the pure graph (and
-   * graph + metadata) find's tail. `orderBy` sorts the WHOLE set by field value
-   * before the page is cut (never the page after), null values last on `asc`
-   * and first on `desc`; without `orderBy` the traversal order stands.
-   */
-  private async pageConnectedIds(params: FindParams<T>, ids: string[]): Promise<Result<T>[]> {
-    const limit = params.limit || 10
-    const offset = params.offset || 0
-    let ordered = ids
-    if (params.orderBy) {
-      const field = params.orderBy
-      const asc = (params.order || 'asc') === 'asc'
-      const valued = await Promise.all(
-        ids.map(async (id) => ({ id, value: await this.metadataIndex.getFieldValueForEntity(id, field) }))
-      )
-      valued.sort((a, b) => {
-        if (a.value == null && b.value == null) return 0
-        if (a.value == null) return asc ? 1 : -1
-        if (b.value == null) return asc ? -1 : 1
-        if (a.value === b.value) return 0
-        const comparison = a.value < b.value ? -1 : 1
-        return asc ? comparison : -comparison
-      })
-      ordered = valued.map((v) => v.id)
+    // Filter existing results to only connected entities
+    if (existingResults.length > 0) {
+      return existingResults.filter(r => connectedIds.has(r.id))
     }
-    const pageIds = ordered.slice(offset, offset + limit)
-    const entitiesMap = await this.batchGet(pageIds)
+
+    // Batch-load connected entities for fast cloud-storage performance
     const results: Result<T>[] = []
-    for (const id of pageIds) {
+    const ids = [...connectedIds]
+    const entitiesMap = await this.batchGet(ids)
+    for (const id of ids) {
       const entity = entitiesMap.get(id)
       if (entity) {
         results.push(this.createResult(id, 1.0, entity))
       }
     }
+
     return results
   }
   
@@ -19625,19 +19455,6 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    *   terminal releases have run.
    */
   async close(): Promise<void> {
-    if (this._pendingEmbedRecovery) {
-      // Settle the background marker fold before the durable steps — its scan
-      // is bounded by the low-water mark (a full scan happens at most once,
-      // on the first open after upgrade).
-      const settleStart = Date.now()
-      await this._pendingEmbedRecovery
-      const settleMs = Date.now() - settleStart
-      if (settleMs >= 1000) {
-        prodLog.info(`[Brainy] close: pending-embed recovery settled in ${settleMs}ms`)
-      }
-      this._pendingEmbedRecovery = null
-    }
-    if (this._pendingEmbedIds.size === 0) await this.writeEmbedLowWater()
     let closeFailure: unknown = null
     try {
       await this.closeDurableSteps()

src/neural/embeddedTypeEmbeddings.ts

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

src/plugin.ts

@@ -411,65 +411,6 @@ 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; apply BEFORE paging so
-   *   `limit` stays exact.
-   * @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 }>>
   getSortedIdsForFilter(filter: any, orderBy: string, order?: 'asc' | 'desc', topK?: number): Promise<string[]>
   getFilterValues(field: string): Promise<string[]>

src/storage/adapters/baseStorageAdapter.ts

@@ -1089,10 +1089,6 @@ 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
@@ -1345,46 +1341,15 @@ export abstract class BaseStorageAdapter implements StorageAdapter {
       return
     }
 
-    // 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
+    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
     }
-
-    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

@@ -2400,15 +2400,8 @@ 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> {
-    // 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}`
+    const tmp = `${filePath}.tmp-${process.pid}-${Date.now()}`
     await fs.promises.writeFile(tmp, contents)
     await fs.promises.rename(tmp, filePath)
   }

src/storage/baseStorage.ts

@@ -2942,33 +2942,19 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         !options.filter.service &&
         !options.filter.metadata
       ) {
-        const sourceIds = Array.isArray(options.filter.sourceId)
-          ? options.filter.sourceId
-          : [options.filter.sourceId]
+        const sourceId = Array.isArray(options.filter.sourceId)
+          ? options.filter.sourceId[0]
+          : options.filter.sourceId
 
-        // 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]
-        )
+        const verbType = Array.isArray(options.filter.verbType)
+          ? options.filter.verbType[0]
+          : options.filter.verbType
 
-        // 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)
-            }
-          }
-        }
+        // 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)
         const filteredVerbs = this.applyVerbMetadataFilters(
-          bySource.filter(v => verbTypes.has(v.verb)),
+          verbsBySource.filter(v => v.verb === verbType),
           options.filter
         )
 
@@ -2999,22 +2985,16 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         !options.filter.service &&
         !options.filter.metadata
       ) {
-        // 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)
+        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
+        )
 
         // Apply pagination
         const paginatedVerbs = verbsBySource.slice(offset, offset + limit)
@@ -3043,22 +3023,16 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         !options.filter.service &&
         !options.filter.metadata
       ) {
-        // 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)
+        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
+        )
 
         // Apply pagination
         const paginatedVerbs = verbsByTarget.slice(offset, offset + limit)
@@ -3087,25 +3061,16 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         !options.filter.service &&
         !options.filter.metadata
       ) {
-        // 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]
+        const verbType = Array.isArray(options.filter.verbType)
+          ? options.filter.verbType[0]
+          : options.filter.verbType
 
-        // 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)
+        // 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
+        )
 
         // Apply pagination
         const paginatedVerbs = verbsByType.slice(offset, offset + limit)

src/transaction/operations/IndexOperations.ts

@@ -14,7 +14,6 @@ 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'
 
 /**
@@ -391,21 +390,13 @@ export class AddToMetadataIndexOperation implements Operation {
     // rollback so add + undo reference the same watermark.
     const generation = this.generationFn?.()
 
-    // 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
-    )
+    // Add to metadata index (skipFlush=true for transaction atomicity)
+    await this.index.addToIndex(this.id, this.entity, true, false, generation)
 
     // Return rollback action
     return async () => {
       // Remove from metadata index
-      await this.index.removeFromIndex(
-        this.id, jsonSafeIndexMetadata(this.entity), generation
-      )
+      await this.index.removeFromIndex(this.id, this.entity, generation)
     }
   }
 }
@@ -441,21 +432,13 @@ export class RemoveFromMetadataIndexOperation implements Operation {
     // Resolve the removal generation once; reuse it for the rollback re-add.
     const generation = this.generationFn?.()
 
-    // 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
-    )
+    // Remove from metadata index
+    await this.index.removeFromIndex(this.id, this.entity, generation)
 
     // Return rollback action
     return async () => {
       // Re-add with original metadata (skipFlush=true)
-      await this.index.addToIndex(
-        this.id, jsonSafeIndexMetadata(this.entity), true, false, generation
-      )
+      await this.index.addToIndex(this.id, this.entity, true, false, generation)
     }
   }
 }

src/utils/jsonSafeIndexMetadata.ts

@@ -1,47 +0,0 @@
-/**
- * @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

@@ -2575,19 +2575,6 @@ 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,

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

@@ -1,111 +0,0 @@
-/**
- * @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/find-connected-order.test.ts

@@ -1,165 +0,0 @@
-/**
- * @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-planner-door.test.ts

@@ -1,137 +0,0 @@
-/**
- * @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/pending-embed-low-water.test.ts

@@ -1,145 +0,0 @@
-/**
- * @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`, and the fold runs behind the doors as a
- * latched background task the worker, `awaitPendingEmbeds()` and `close()`
- * wait on. 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, behind the doors', () => {
-  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)
-    await (brain2 as any)._pendingEmbedRecovery
-    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('open arms the fold as a background latch; awaitPendingEmbeds waits on it', 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 latch exists the moment init() returns (writable filesystem brain)…
-    expect((brain2 as any)._pendingEmbedRecovery).not.toBeNull()
-    // …and the barrier settles it before answering.
-    await brain2.awaitPendingEmbeds()
-    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/related-verb-array.test.ts

@@ -1,89 +0,0 @@
-/**
- * @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/transact-edge-delete-bigint-aliasing.test.ts

@@ -1,184 +0,0 @@
-/**
- * @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([[], []])
-  })
-})