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 {
@@ -4204,19 +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,
+   * crossing. The seam's metadata is JSON-safe BY CONTRACT (a native provider
-   * which the metadata-index transaction operations ALSO apply at execute
+   * serializes it; u64 ints as Number corrupt above 2^53) — but
-   * and rollback time. This plan-time wrap alone proved insufficient: it
+   * {@link resolveVerbEndpointInts} MIRRORS the resolved endpoint ints onto
-   * returns the same reference when the record is clean, and `transact()`'s
+   * the verb object itself as BigInt (`verb.sourceInt`/`targetInt`), so a
-   * delete legs share that reference with a graph-retraction op whose
+   * verb object reused as index metadata carried BigInts into
-   * execute-time endpoint resolution mirrors BigInt ints onto it (the full
+   * JSON.stringify, which throws, aborting the whole transaction (found by
-   * aliasing story lives on the leaf module's doc).
+   * 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(

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
+    try {
-    // a burst of writes used to launch one persist per change, all in flight
+      // Persist to storage (implemented by subclass)
-    // together. Two of them inside the same millisecond shared the atomic
+      await this.persistCounts()
-    // writer's temp path (`.tmp-<pid>-<ms>`): both wrote it, the first rename
+      this.pendingCountPersist = false
-    // consumed it, the second rename found nothing — ENOENT, ~1,500 times a
+    } catch (error) {
-    // day on a busy production brain, with a full ledger write per change
+      console.error('CRITICAL: Failed to flush counts to storage:', error)
-    // behind it. Now exactly one persist runs at a time; requests that arrive
+      // Keep pending flag set so we retry on next operation
-    // while it runs collapse into ONE trailing persist that carries the final
+      throw error
-    // 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

@@ -2400,15 +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
+    const tmp = `${filePath}.tmp-${process.pid}-${Date.now()}`
-    // one millisecond shared this path, and the loser's rename found the
-    // winner had already moved it (ENOENT). The sequence makes every call's
-    // temp path its own.
-    const tmp = `${filePath}.tmp-${process.pid}-${Date.now()}-${++FileSystemStorage.atomicWriteSeq}`
     await fs.promises.writeFile(tmp, contents)
     await fs.promises.rename(tmp, filePath)
   }

src/storage/baseStorage.ts

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

@@ -14,7 +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:
+    // Add to metadata index (skipFlush=true for transaction atomicity)
-    // the entity reference this op holds can be mutated between plan and
+    await this.index.addToIndex(this.id, this.entity, true, false, generation)
-    // 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(
+      await this.index.removeFromIndex(this.id, this.entity, generation)
-        this.id, jsonSafeIndexMetadata(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
+    // Remove from metadata index
-    // legs hand this op the SAME verb object the graph-retraction op's
+    await this.index.removeFromIndex(this.id, this.entity, generation)
-    // 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(
+      await this.index.addToIndex(this.id, this.entity, true, false, generation)
-        this.id, jsonSafeIndexMetadata(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
-}

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/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([[], []])
-  })
-})