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.
