feat: enhance database transactions, add Makefiles, and improve Docker setup

- Refactored database batch operations to ensure transaction atomicity and simplify nested structure.
- Added `Makefile` for `knowledge-base` and `llm-gateway` modules to streamline development workflows.
- Simplified `Dockerfile` for `llm-gateway` by removing multi-stage builds and optimizing dependencies.
- Improved code readability in `collection_manager` and `failover` modules with refined logic.
- Minor fixes in `test_server` and Redis health check handling for better diagnostics.

mcp-servers/knowledge-base/server.py

@@ -193,7 +193,7 @@ async def health_check() -> dict[str, Any]:
     # Check Redis cache (non-critical - degraded without it)
     try:
         if _embeddings and _embeddings._redis:
-            await _embeddings._redis.ping()
+            await _embeddings._redis.ping()  # type: ignore[misc]
             status["dependencies"]["redis"] = "connected"
         else:
             status["dependencies"]["redis"] = "not initialized"