Adds a reserved, top-level `visibility` field (mirrors the subtype rollout):
'public' (default, surfaced) | 'internal' (developer app-internal — hidden from
default find/count/stats, opt-in via includeInternal) | 'system' (Brainy
plumbing, library-set only).
Fixes a real leak: the VFS root entity counted in getNounCount() and appeared in
find() (a fresh brain reported 1 entity). It is now visibility:'system' →
excluded from every user-facing surface. Developers also get a first-class
hidden-unless-asked tier (e.g. learned internals vs user-exposed data).
- Reserved (RESERVED_ENTITY_FIELDS / RESERVED_RELATION_FIELDS) — spoof-proof from metadata.
- Threaded through add/relate/update/transact; surfaced top-level on reads.
- Default exclusion in counts (baseStorage), find()/related() (hard candidate
filter via excludeVisibility — keeps topK/limit correct), and stats;
includeInternal/includeSystem opt-ins.
- VFS root marked 'system'.
Tests: visibility.test.ts 17/17 (fresh-brain getNounCount()===0, internal hidden
+ opt-in, verb symmetry, top-level surfacing, metadata-spoof rejection). Unit
1431 green; count-synchronization integration now passes (off-by-one fixed).
The __words__ keyword index stores 50-5000 entries per entity (one per
word), which inflated avg entries/entity well above the corruption
threshold of 100. This caused:
1. validateConsistency() to falsely detect corruption on every startup,
triggering unnecessary clearAllIndexData() + rebuild() cycles
2. getStats() to log false "Metadata index may be corrupted" warnings
and report inflated totalEntries/totalIds stats
Both methods now skip __words__ when counting, so stats and health
checks reflect metadata fields only (noun, type, createdAt, etc.).
Keyword search is unaffected since the __words__ field index itself
is not modified.
CRITICAL BUG FIX: Workshop team reported 1,360,000+ entities loaded instead of 3,593
(378x multiplier), causing 15-20 minute startup times making app completely unusable.
## Root Cause
Pagination implementation had fundamental cursor/offset mismatch across codebase:
1. HNSW/Graph rebuilds passed `cursor` parameter
2. Storage methods accepted `cursor` but never used it, defaulted offset=0
3. Every pagination call returned same first N entities infinitely
4. hasMore calculation bug (>= instead of >) caused true infinite loop
## Fixes Applied (15 bugs across 5 files)
### src/storage/baseStorage.ts (5 fixes)
- Line 1086: Document cursor parameter currently ignored (offset-based for now)
- Line 1191: Fix hasMore (>= to >) in getNounsWithPagination
- Line 1221: Document cursor parameter currently ignored
- Line 1305: Fix hasMore (>= to >) in getVerbsWithPagination
- Line 1631: Fix hasMore (>= to >) in getVerbs
### src/storage/adapters/optimizedS3Search.ts (2 fixes)
- Line 110: Fix hasMore (>= to >) for nouns
- Line 193: Fix hasMore (>= to >) for verbs
### src/hnsw/typeAwareHNSWIndex.ts (2 fixes)
- Line 455: Change cursor to offset-based pagination
- Line 533: Increment offset instead of updating cursor
### src/hnsw/hnswIndex.ts (2 fixes)
- Line 1095: Change cursor to offset-based pagination
- Line 1164: Increment offset instead of updating cursor
### src/utils/rebuildCounts.ts (4 fixes)
- Line 67: Change cursor to offset for nouns
- Line 85: Increment offset for nouns
- Line 98: Change cursor to offset for verbs
- Line 115: Increment offset for verbs
## Impact
BEFORE v5.7.11:
- ❌ Loading 1,360,000+ entities (378x multiplier)
- ❌ 15-20 minute startup times
- ❌ Application completely unusable
- ❌ Workshop team blocked from using disableAutoRebuild
AFTER v5.7.11:
- ✅ Loads correct entity count (3,593 entities)
- ✅ Fast startup (< 10 seconds for 3,600 entities)
- ✅ disableAutoRebuild works correctly
- ✅ No more infinite pagination loops
## Verification
Test with 50 entities shows:
- ✅ Correct count: 50 documents + 1 collection = 51 entities
- ✅ No 378x multiplier
- ✅ No infinite loop
- ✅ Fast rebuild completion
Resolves critical production blocker for Workshop team.
## Phase 2 (Future: v5.8.0)
Implement proper cursor-based pagination for stateless billion-scale support.
Current fix uses offset-based pagination which is sufficient for datasets
up to 10M entities.
Related: BRAINY_STARTUP_PERFORMANCE_BUG.md, BRAINY_V5_7_9_HNSW_BUG.md
Fixed critical bug where entity and relationship counts were not being tracked correctly
during add(), relate(), and import() operations. The root cause was a race condition where
count increment code tried to read metadata before it was saved to storage.
Core Fixes:
- Modified baseStorage.saveNounMetadata_internal to increment counts AFTER metadata is saved
- Modified baseStorage.saveVerbMetadata_internal to increment verb counts AFTER metadata is saved
- Added verb type to VerbMetadata to avoid circular dependency during count tracking
- Refactored verb count methods to prevent mutex deadlocks (synchronous base + async Safe wrapper)
Storage Adapter Cleanup:
- Removed broken count increment code from FileSystemStorage, GcsStorage, R2Storage, AzureBlobStorage
- Updated MemoryStorage comments to reflect centralized fix
- All count tracking now centralized in baseStorage (fixes ALL adapters automatically)
New Utilities:
- Added rebuildCounts utility to repair corrupted counts.json from actual storage data
- Added comprehensive integration tests for count synchronization across all operations
Verification:
- All 8 storage adapters verified (FileSystem, GCS, Memory, S3Compatible, R2, Azure, OPFS, TypeAware)
- All code paths verified (add, relate, import, batch, update, delete)
- 599 tests passing (no regressions)
- No deadlocks (tests complete in 6s vs 150s+)
Fixes#1 and #2 reported by Workshop team
