chore: harden knowledge graph storage and clear common clippy warnings

Enforce stable 1:1 entity embeddings, relationship endpoint auth, and
user-scoped deletes; align schemas/migrations and resolve common crate
clippy findings.

common/migrations/20260528_000002_knowledge_graph_storage_hardening.surql

@@ -0,0 +1,33 @@
+-- Harden knowledge entity embeddings and graph storage invariants.
+
+DEFINE FIELD IF NOT EXISTS source_id ON knowledge_entity_embedding TYPE string;
+
+-- Backfill denormalized source_id from the linked entity.
+FOR $emb IN (SELECT * FROM knowledge_entity_embedding WHERE source_id = NONE OR source_id = '') {
+    LET $entity = (SELECT source_id FROM $emb.entity_id)[0];
+    IF $entity != NONE {
+        UPDATE $emb.id SET source_id = $entity.source_id;
+    }
+};
+
+-- Re-key embeddings so record id matches entity id (stable 1:1 identity).
+FOR $emb IN (SELECT * FROM knowledge_entity_embedding) {
+    LET $entity_key = record::id($emb.entity_id);
+    LET $canonical = type::thing('knowledge_entity_embedding', $entity_key);
+    IF $emb.id != $canonical {
+        UPSERT $canonical CONTENT {
+            entity_id: $emb.entity_id,
+            embedding: $emb.embedding,
+            user_id: $emb.user_id,
+            source_id: $emb.source_id,
+            created_at: $emb.created_at,
+            updated_at: $emb.updated_at
+        };
+        DELETE $emb.id;
+    }
+};
+
+REMOVE INDEX IF EXISTS knowledge_entity_embedding_entity_id_idx ON knowledge_entity_embedding;
+DEFINE INDEX IF NOT EXISTS knowledge_entity_embedding_entity_id_idx ON knowledge_entity_embedding FIELDS entity_id UNIQUE;
+DEFINE INDEX IF NOT EXISTS knowledge_entity_embedding_source_id_idx ON knowledge_entity_embedding FIELDS source_id;
+DEFINE INDEX IF NOT EXISTS knowledge_entity_user_source_idx ON knowledge_entity FIELDS user_id, source_id;

common/migrations/definitions/20260528_000002_knowledge_graph_storage_hardening.json

@@ -0,0 +1 @@
+{"schemas":"--- original\n+++ modified\n@@ -68,7 +68,7 @@\n\n # Defines the schema for the 'knowledge_entity' table.\n\n-DEFINE TABLE IF NOT EXISTS knowledge_entity SCHEMALESS;\n+DEFINE TABLE IF NOT EXISTS knowledge_entity SCHEMAFULL;\n\n # Standard fields\n DEFINE FIELD IF NOT EXISTS created_at ON knowledge_entity TYPE datetime;\n@@ -90,6 +90,7 @@\n -- DEFINE INDEX IF NOT EXISTS idx_embedding_entities ON knowledge_entity FIELDS embedding HNSW DIMENSION 1536;\n DEFINE INDEX IF NOT EXISTS knowledge_entity_source_id_idx ON knowledge_entity FIELDS source_id;\n DEFINE INDEX IF NOT EXISTS knowledge_entity_user_id_idx ON knowledge_entity FIELDS user_id;\n+DEFINE INDEX IF NOT EXISTS knowledge_entity_user_source_idx ON knowledge_entity FIELDS user_id, source_id;\n DEFINE INDEX IF NOT EXISTS knowledge_entity_entity_type_idx ON knowledge_entity FIELDS entity_type;\n DEFINE INDEX IF NOT EXISTS knowledge_entity_created_at_idx ON knowledge_entity FIELDS created_at;\n\n@@ -102,6 +103,7 @@\n DEFINE FIELD IF NOT EXISTS created_at ON knowledge_entity_embedding TYPE datetime;\n DEFINE FIELD IF NOT EXISTS updated_at ON knowledge_entity_embedding TYPE datetime;\n DEFINE FIELD IF NOT EXISTS user_id ON knowledge_entity_embedding TYPE string;\n+DEFINE FIELD IF NOT EXISTS source_id ON knowledge_entity_embedding TYPE string;\n\n -- Custom fields\n DEFINE FIELD IF NOT EXISTS entity_id ON knowledge_entity_embedding TYPE record<knowledge_entity>;\n@@ -109,8 +111,9 @@\n\n -- Indexes\n -- DEFINE INDEX IF NOT EXISTS idx_embedding_knowledge_entity_embedding ON knowledge_entity_embedding FIELDS embedding HNSW DIMENSION 1536;\n-DEFINE INDEX IF NOT EXISTS knowledge_entity_embedding_entity_id_idx ON knowledge_entity_embedding FIELDS entity_id;\n+DEFINE INDEX IF NOT EXISTS knowledge_entity_embedding_entity_id_idx ON knowledge_entity_embedding FIELDS entity_id UNIQUE;\n DEFINE INDEX IF NOT EXISTS knowledge_entity_embedding_user_id_idx ON knowledge_entity_embedding FIELDS user_id;\n+DEFINE INDEX IF NOT EXISTS knowledge_entity_embedding_source_id_idx ON knowledge_entity_embedding FIELDS source_id;\n\n # Defines the schema for the 'message' table.\n\n@@ -135,19 +138,17 @@\n # Defines the 'relates_to' edge table for KnowledgeRelationships.\n # Edges connect nodes, in this case knowledge_entity records.\n\n-# Define the edge table itself, enforcing connections between knowledge_entity records\n-# SCHEMAFULL requires all fields to be defined, maybe start with SCHEMALESS if metadata might vary\n-DEFINE TABLE IF NOT EXISTS relates_to SCHEMALESS TYPE RELATION FROM knowledge_entity TO knowledge_entity;\n+DEFINE TABLE IF NOT EXISTS relates_to SCHEMAFULL TYPE RELATION FROM knowledge_entity TO knowledge_entity;\n+\n+DEFINE FIELD IF NOT EXISTS in ON relates_to TYPE record<knowledge_entity>;\n+DEFINE FIELD IF NOT EXISTS out ON relates_to TYPE record<knowledge_entity>;\n\n-# Define the metadata field within the edge\n # RelationshipMetadata is a struct, store as object\n DEFINE FIELD IF NOT EXISTS metadata ON relates_to TYPE object;\n+DEFINE FIELD IF NOT EXISTS metadata.user_id ON relates_to TYPE string;\n+DEFINE FIELD IF NOT EXISTS metadata.source_id ON relates_to TYPE string;\n+DEFINE FIELD IF NOT EXISTS metadata.relationship_type ON relates_to TYPE string;\n\n-# Optionally, define fields within the metadata object for stricter schema (requires SCHEMAFULL on table)\n-# DEFINE FIELD IF NOT EXISTS metadata.user_id ON relates_to TYPE string;\n-# DEFINE FIELD IF NOT EXISTS metadata.source_id ON relates_to TYPE string;\n-# DEFINE FIELD IF NOT EXISTS metadata.relationship_type ON relates_to TYPE string;\n-\n # Add indexes based on query patterns (delete_relationships_by_source_id, get_knowledge_relationships)\n DEFINE INDEX IF NOT EXISTS relates_to_metadata_source_id_idx ON relates_to FIELDS metadata.source_id;\n DEFINE INDEX IF NOT EXISTS relates_to_metadata_user_id_idx ON relates_to FIELDS metadata.user_id;\n","events":null}