feat: add lightrag-mcp MCP server + agent tooling

- Add AGENTS.md with repo guidelines
- Add lightrag-mcp: FastMCP server exposing insert_documents() + query_documents()
  to LLM agents via stdio transport, talks to LightRAG REST API
- Add scripts/patch-vllm-cpu.py for CPU inference patching
- Add .env.vllm for vLLM configuration
- Update flake.nix with expanded dev shell
- Update .env.lightrag
- Remove CLAUDE.md (replaced by AGENTS.md)

AGENTS.md

@@ -0,0 +1,66 @@
+# RAGS
+
+Private learning tool. Ingest study materials → knowledge graph → query → export Anki flashcards.
+
+Two systems:
+- **LightRAG** (`lightrag/`) — graph-based RAG server (primary interface)
+- **Graphiti** (`graphiti/`) — temporal knowledge graph library (Python library only, needs Neo4j)
+
+## Quick Start
+
+```sh
+# Ollama must be running first on :11434 with:
+#   qwen3:0.6b       (LLM)
+#   qwen3-embedding:0.6b  (embeddings)
+
+# Start LightRAG only (LLM + embeddings handled externally by Ollama)
+nix run .#start
+# → http://localhost:9621/webui  (React frontend)
+# → http://localhost:9621/docs   (Swagger API)
+
+# Graphiti needs Neo4j running first
+nix run .#neo4j-start   # separate terminal
+nix develop .#graphiti
+```
+
+**Always enter via `nix develop` from repo root** — never activate venvs directly. The shellHook sources `.env.lightrag` and sets `LD_LIBRARY_PATH`.
+
+## Configuration
+
+### `.env.lightrag`
+**Restart LightRAG after changes.**
+
+| Var | Value |
+|-----|-------|
+| `LLM_BINDING` | `ollama` |
+| `LLM_MODEL` | `qwen3:0.6b` |
+| `LLM_BINDING_HOST` | `http://localhost:11434` |
+| `EMBEDDING_BINDING` | `ollama` |
+| `EMBEDDING_MODEL` | `qwen3-embedding:0.6b` |
+| `EMBEDDING_DIM` | `1024` |
+
+Verify embedding works:
+```sh
+curl -s http://localhost:11434/api/embed \
+  -H "Content-Type: application/json" \
+  -d '{"model":"qwen3-embedding:0.6b","input":"test"}'
+```
+
+**Critical:** If `EMBEDDING_DIM` changes, delete `rag_storage/` before restarting — old vectors are incompatible.
+
+## LightRAG Storage
+File-based by default (`JsonKVStorage`, `NanoVectorDBStorage`, `NetworkXStorage`). All data in `rag_storage/` (gitignored). Safe to delete to reset.
+
+## Nix / NixOS Notes
+- `UV_PYTHON` pinned to nix-provided Python 3.12 (system has 3.14)
+- `LD_LIBRARY_PATH` set in shellHook for native wheels
+- LightRAG installs with `--extra api --extra offline-llm`
+- WebUI (React/Bun) built on first shell entry if `lightrag/lightrag/api/webui/` missing
+
+## Known Issue: Pipeline Stuck
+
+After config changes, pipeline may show `busy: true` with pending async locks. Symptoms:
+- `GET /documents/pipeline_status` returns `busy: true`, `request_pending: true`
+- New inserts stay at `status: pending`
+
+Fix: delete `rag_storage/`, restart. Or `POST /documents/cancel_pipeline`.