Cortex and other first-party plugins need a shared contract for reading
fields off HNSWNounWithMetadata. Exporting from /internals keeps a single
source of truth and prevents the shape contract from drifting between
packages.
Muse reported that find({ orderBy: 'createdAt' }) silently returned the
wrong order: getFieldValueForEntity read noun.metadata[field] for
timestamp fields, but getNoun() destructures standard fields to the top
level, so the read always returned undefined and the sort collapsed to
insertion order.
The fix introduces a single source of truth for reading fields off an
entity. STANDARD_ENTITY_FIELDS + resolveEntityField() in coreTypes.ts
encode the "standard fields top-level, custom fields nested" contract
in one place. getFieldValueForEntity now uses the helper and routes
through a named BUCKETED_INDEX_FIELDS set instead of a hardcoded
timestamp if-chain — filtered sort on createdAt/updatedAt now works.
Unfiltered orderBy is explicitly rejected with a clear error pointing
callers at the right pattern. A scalable, unfiltered-sort-capable
time-ordered segment index is tracked as a separate follow-up.
Root cause: metadata index failed to reconstruct after deploy restart
because the field registry file (__metadata_field_registry__) was lost
during an interrupted flush. init() silently assumed the workspace was
empty even though 5000+ entities existed on disk.
Fix 1 (root cause): init() now probes storage for entities when field
registry is missing. If entities exist, triggers rebuild instead of
silently skipping. Never trusts a missing registry as "empty."
Fix 2 (safety net): after rebuildIndexesIfNeeded(), verifies metadata
index entry count matches storage entity count. Forces second rebuild
if mismatch detected.
Fix 3 (prevention): flush() now always saves field registry and
EntityIdMapper, even when no dirty fields exist. These tiny files are
the critical link that init() needs to discover persisted indices.
Fix 5 (safe rebuild): rebuild() no longer deletes the field registry
file before rewriting. If rebuild fails partway, the registry survives
for the next init() to discover and re-trigger rebuild.
Fix 6 (collision guard): EntityIdMapper init() warns when mapper file
is missing but entities exist on disk, preventing silent ID collisions
from nextId starting at 1.
commit() previously defaulted captureState to false, creating commits
with NULL_HASH tree that could never be restored from. Now:
- flush() runs first to persist deferred HNSW nodes, count batches,
and index state before snapshotting
- captureState defaults to true, creating real content-addressed trees
- captureState: false still available for lightweight metadata-only commits
UnifiedCache.setMaxSize() allows runtime resizing of the cache maximum.
When the new limit is smaller than current usage, lowest-value items are
evicted until the cache fits. Used by Cortex's ResourceManager to
rebalance cache vs instance memory as brainy instances are created and
evicted in multi-tenant deployments.
Also adds getMaxSize() for observability.
EmbeddingManager constructor logged 'Using Q8 precision (WASM)' before
plugins had a chance to register a native embedder. Deferred logging to
init() so the startup message reflects the actual embedding engine.
addMany() now temporarily switches the HNSW index to deferred persist
mode during the batch loop. Previously, each add() triggered ~16-20
saveHNSWData calls for modified neighbors (each a read→gzip→atomic-write
cycle). For 450 items this was ~8,100 individual storage writes.
With deferred mode, dirty node IDs are collected in a Set during the
batch and flushed once at the end — deduplicating repeated neighbor
updates. A node modified by insert #3 and again by insert #47 is
written only once.
Also adds setPersistMode() to TypeAwareHNSWIndex, propagating mode
changes to all existing type-specific sub-indexes.
The storage config type only exposed { type, options, branch } but plugin
storage factories (e.g. Cortex mmap) read rootDirectory from the top level
of the config object. This caused undefined storage paths when Cortex was
active. The underlying StorageOptions interface already declares
rootDirectory — this aligns BrainyConfig.storage to match.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
SSTable.calculateChecksum() used require('crypto') which breaks in ESM
environments and Bun. Replace with top-level import { createHash } from
'node:crypto' — SSTable is Node-only (LSM-tree filesystem storage) so
a direct node:crypto import is appropriate.
Code blocks with Unicode box-drawing characters render poorly in web
doc viewers — font alignment breaks and the styled container creates
a visual box-in-a-box. Replaced with a bullet list (before) and a
bold statement (after) that render cleanly at any size and theme.
Replace flat 15-row table with a Before/After ASCII diagram plus a
capability grid (Search/Graph/Filter/VFS/Branch/Import) with competitors
grouped by category. Add new What Can You Build? section with generic
use cases and Built with Brainy showcase. Tighten header copy.
Adds docs/eli5.md — a jargon-free explanation of Brainy and Cortex
using everyday analogies (smart librarian, turbocharger). Targets
non-technical readers who want to understand the project before diving
into the API. Links added at the top of README and in the Documentation
section index.
All code examples in installation.md and quick-start.md were tagged
as javascript — converted to typescript throughout.
quick-start.md also gets explicit type annotations:
- reactId/nextId declared as string (return type of brain.add)
- results declared as FindResult[]
- results[0].data and results[0].score shown in console.log example
Add YAML frontmatter (slug, public, category, template, order) to 8
existing docs and 2 new getting-started guides (installation, quick-start).
Include docs/**/*.md in npm package files so the portal sync-docs script
can read them from node_modules after publish.
Update CLAUDE.md with docs pipeline trigger phrases and release checklist.
Three bugs caused deleted entities to persist in the metadata index:
1. idMapper never cleaned up — EntityIdMapper accumulated UUID→int mappings
permanently. idMapper.getAllIntIds() is used as the universe for ne and
exists:false operators, so deleted entities returned in those queries
indefinitely. Fix: removeFromIndex() now calls idMapper.remove(id) and
idMapper.flush() after all bitmap operations complete (must be last because
removeFromChunk() reads idMapper.getInt(id) internally).
2. Optional fields indexed as __NULL__ but never unindexed — entityForIndexing
in add() included confidence, weight, and createdBy as explicit keys even
when undefined. Object.entries() preserves undefined-valued keys so
extractIndexableFields() indexed them as '__NULL__' bitmap entries.
storageMetadata omitted those keys via conditional spreading, so
removeFromIndex() passed a structure without those keys and never cleaned
them up. Fix: entityForIndexing now uses conditional spreading for
confidence, weight, and createdBy matching storageMetadata exactly.
3. result.successful updated before transaction commits — deleteMany() pushed
ids to result.successful inside the transaction builder, before
transaction.execute() ran. A rollback would leave result.successful
containing ids that were never actually deleted. Fix: queued ids are held
in a local chunkQueued array and moved to result.successful only after
executeTransaction() resolves without throwing.
Adds regression test suite (14 tests) covering delete() and deleteMany() for
type-index cleanup, ne operator, exists:false operator, optional-field indexing,
and partial deletion correctness.
Reported by wickworks team.
The pkg/ directory containing the Candle WASM binary was excluded from
the npm tarball because it contained its own package.json and .gitignore
(with `*` pattern). The build:copy-wasm script now skips these files
when copying to dist/, ensuring candle_embeddings.js/.wasm are included.
Also adds ./embeddings/wasm export subpath for clean ESM imports.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add a write-time incremental aggregation engine that maintains running
totals on every add/update/delete for O(1) read performance. Integrates
into brain.find({ aggregate }) for a unified query API.
Core features:
- AggregationIndex with defineAggregate()/removeAggregate() API
- Five aggregation operations: SUM, COUNT, AVG, MIN, MAX
- GROUP BY with multiple dimensions including time windows
- Time window bucketing: hour, day, week, month, quarter, year, custom
- Materialization of results as NounType.Measurement entities
- Debounced persistence of definitions and state to storage
- Definition change detection via FNV-1a hashing with auto-rebuild
- Infinite loop prevention for materialized entities
- 'aggregation' plugin provider key for native acceleration
- Lazy initialization (created on first defineAggregate() call)
- 73 tests (unit + integration) covering all functionality
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Contributor-friendly CLAUDE.md with setup, conventions, and architecture
overview. Comprehensive skills/architecture.md verified against actual
codebase covering all 31 source directories, 38+ exports, and major
subsystems (distributed, transactions, neural, CLI, MCP, COW, etc).
Remove CLAUDE.md from .gitignore since the new version is designed
for public contributors.
- Store data opaquely in add() and update() instead of spreading object
properties into top-level metadata. data is for semantic search (HNSW),
metadata is for structured where-filter queries (MetadataIndex).
- Fix numeric range queries in MetadataIndex — use numeric-aware comparison
instead of lexicographic string comparison for normalized values.
- Add data field to RelateParams and Relation types for relationship content.
- Add where.type → where.noun alias in metadata-only find() path.
- Rewrite README: focused ~350 lines from 791, quick start first, feature
showcase with mini-snippets, organized doc links, no version callouts.
- Add DATA_MODEL.md and QUERY_OPERATORS.md reference docs.
- Remove 10 outdated/redundant doc files consolidated into API reference.
- Improve JSDoc on Entity, Relation, AddParams, FindParams, and core methods.
- Fix tests asserting data properties appear in metadata (data model violation).
- Deprecate verb.source/target in favor of from/to (public) and sourceId/targetId (storage).
Plugins are no longer auto-detected. Updated README and PLUGINS.md
to show explicit plugins config, document all config values, and
fix manual registration example to use brain.use() API.
relate() was setting verb.source = fromEntity.type (a NounType like
"concept") instead of the entity UUID. Cortex's graph index indexes by
verb.source, so lookups by UUID found nothing — causing in-session
reads to return 0 results.
Also fixes:
- PathResolver calling private getIdsFromChunks() → public getIds()
- Plugin auto-detection removed; cortex loads only via explicit config
- GraphVerb types accept number timestamps and sourceId/targetId aliases
- Dead autoDetect() method removed from PluginRegistry
- In-session regression tests added for getRelations after relate()
GraphAdjacencyIndex.flush() was a no-op — LSM MemTables were never
written to SSTables for datasets under the 100K auto-flush threshold.
This caused readdir, getRelations, and getDescendants to return empty
results after close + reopen.
Three fixes:
- LSMTree.get(): merge MemTable + SSTable results (data spans both
after flush, old early-return missed SSTable data)
- GraphAdjacencyIndex.flush(): actually flush all 4 LSM-trees
- GraphAdjacencyIndex.close(): close all 4 trees (was only closing 2)
Also: brain.close() and shutdown hooks now call close() on graphIndex,
HNSW index, and metadataIndex to release timers and file handles.
Shutdown/close/flush now properly flushes all 4 components in parallel:
metadataIndex, graphIndex, HNSW dirty nodes, and storage counts. Previously
only counts were flushed, causing native provider data loss on restart.
Also:
- Wire roaring, msgpack, entityIdMapper provider consumption from plugins
- Fix allOf filter O(n²) intersection → O(n) Set-based
- Fix ne/exists negation filter to use Set-based exclusion
- Add setMsgpackImplementation() swap in SSTable for native msgpack
- Add setRoaringImplementation() swap for native CRoaring bitmaps
- Add getAllIntIds() to EntityIdMapper for bitmap operations
- Remove TypeAwareHNSWIndex from default index creation path
- Export memory detection utilities from internals
- Clean up 26 permanently-skipped dead tests
