feat: add query/retrieval FlowProcessor services and missing runner scripts

Wire up the query and retrieval side of the pipeline so the agent can
answer questions from stored knowledge:

- Triples query service (FalkorDB) — all SPO pattern queries via NATS
- Graph embeddings query service (Qdrant) — entity vector similarity
- Document embeddings query service (Qdrant) — chunk vector similarity
- Graph RAG service — full concept→entity→traverse→score→synthesize pipeline
- Document RAG service — embed→find chunks→synthesize pipeline
- Runner scripts for chunker, extractor, embeddings (missing from Phase 5)
- Add DocumentEmbeddingsRequest/Response schema types
- Add RAG prompt templates (extract-concepts, edge-scoring, synthesize)
- Add graph/doc embeddings query topics to seed config + flow manager
- Add all pipeline/query/retrieval services to docker-compose
- 8 new runner scripts, 8 new pnpm script aliases

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

ts/package.json

@@ -21,7 +21,15 @@
     "llm:ollama": "tsx scripts/run-ollama.ts",
     "pdf-decoder": "tsx scripts/run-pdf-decoder.ts",
     "triples-store": "tsx scripts/run-triples-store.ts",
-    "graph-embeddings-store": "tsx scripts/run-graph-embeddings-store.ts"
+    "graph-embeddings-store": "tsx scripts/run-graph-embeddings-store.ts",
+    "chunker": "tsx scripts/run-chunker.ts",
+    "extractor": "tsx scripts/run-extractor.ts",
+    "embeddings": "tsx scripts/run-embeddings.ts",
+    "triples-query": "tsx scripts/run-triples-query.ts",
+    "graph-embeddings-query": "tsx scripts/run-graph-embeddings-query.ts",
+    "doc-embeddings-query": "tsx scripts/run-doc-embeddings-query.ts",
+    "graph-rag": "tsx scripts/run-graph-rag.ts",
+    "document-rag": "tsx scripts/run-document-rag.ts"
   },
   "devDependencies": {
     "nats": "^2.29.0",