fix(vectors): a zero-norm vector is not a vector, canonical side included, plus the sanctioned unvector door

The engine-pair seam law: a zero-norm vector never crosses an engine
boundary. The index belt already refused to insert one, but the canonical
write and the vectored-noun ledger still counted it, so a near-empty store
whose only vectored row was zero-norm read "1 canonical vectored vs 0
indexed" and threw a not-ready error at open, and a store's own legacy
zero-norm VFS root could trip the same gate before its VFS-init-time cure
ever ran.

- add()/update() (single and transact()) now normalize an explicit
  real all-zero vector to the unvectored [] shape before the dimension
  pin, the ledger flag, and the index ops ever see it (loud, one warn per
  write, canonical write still succeeds).
- The legacy counts.json derivation walk (scanVectoredNounCount) excludes
  a persisted zero-norm row, matching the live ledger's definition.
- A legacy zero-norm VFS root now migrates at open, before the vector-leg
  gate evaluates, via one O(1) fixed-path read (torn-tolerant — skips
  rather than aborting init on a torn root, letting the recovery walk
  heal it) — independent of whether a VirtualFileSystem is ever
  constructed this session.
- update({ id, vector: [] }) (and the same op inside transact()) is now
  the sanctioned, idempotent unvector door: index removal, exactly-once
  ledger decrement, no re-embed, and it clears a pending deferred-embed
  marker rather than leaving it to re-vectorize the row later. The
  combination with deferEmbedding is a typed refusal.
- JsHnswVectorIndex.rebuild() now skips a zero-norm/empty persisted
  vector when repopulating from canonical (the same belt the live
  add/replace paths already had), and health()'s index-parity check now
  compares HNSW size against the vectored-noun ledger rather than the
  raw metadata-entry count, since a store's VFS root is permanently
  unvectored by design.

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

src/storage/adapters/fileSystemStorage.ts

@@ -19,6 +19,7 @@ import {
 import { getBrainyVersion } from '../../utils/index.js'
 import { isAbsentError } from '../../utils/errorClassification.js'
 import { prodLog } from '../../utils/logger.js'
+import { isZeroNormVector } from '../../utils/distance.js'
 import {
   TornRecordError,
   isUnparseablePayloadError,
@@ -2841,14 +2842,20 @@ export class FileSystemStorage extends BaseStorage {
   }
 
   /**
-   * Count canonical nouns holding a REAL (non-empty) vector — the vectored-
-   * noun ledger scalar. UNLIKE {@link scanCanonicalEntities}, presence
-   * cannot be decided from the id-directory listing alone: a deferred-embed
-   * noun's `vectors.json` EXISTS (written at `add()` time with `vector: []`)
-   * until its embed LANDS, so this walk reads every noun's `vectors.json`
-   * CONTENT — O(nouns) reads, not O(ids) listing. Used ONLY for a one-time
-   * legacy-counts.json derivation or a lost/corrupted counts.json recovery;
-   * the result is persisted so this scan never repeats.
+   * Count canonical nouns holding a REAL (non-empty, non-zero-norm) vector —
+   * the vectored-noun ledger scalar. UNLIKE {@link scanCanonicalEntities},
+   * presence cannot be decided from the id-directory listing alone: a
+   * deferred-embed noun's `vectors.json` EXISTS (written at `add()` time
+   * with `vector: []`) until its embed LANDS, so this walk reads every
+   * noun's `vectors.json` CONTENT — O(nouns) reads, not O(ids) listing.
+   * ZERO-NORM LAW: a real all-zero vector is not a vector — it never counts
+   * here either (Brainy's write paths normalize an explicit zero-norm
+   * vector to `[]` at write time, but a store created before that fix may
+   * still carry legacy all-zero rows on disk; this derivation must agree
+   * with the live ledger's definition of "vectored" regardless of when the
+   * row was written). Used ONLY for a one-time legacy-counts.json derivation
+   * or a lost/corrupted counts.json recovery; the result is persisted so
+   * this scan never repeats.
    */
   private async scanVectoredNounCount(): Promise<number> {
     const base = path.join(this.rootDir, 'entities', 'nouns')
@@ -2862,7 +2869,12 @@ export class FileSystemStorage extends BaseStorage {
         for (const entry of ids) {
           if (!entry.isDirectory()) continue
           const record = await this.readEntityVectorRaw(path.join(shardPath, entry.name))
-          if (record && Array.isArray(record.vector) && record.vector.length > 0) {
+          if (
+            record &&
+            Array.isArray(record.vector) &&
+            record.vector.length > 0 &&
+            !isZeroNormVector(record.vector)
+          ) {
             vectored++
           }
         }