style: apply ruff lint --fix + ruff format across the tree

perf(mcp): HTTP transport core — add_mcp_http on agent/tool_manager + adata cache + instrumentation

Surface exceptions from add_mcp_server's outer try/except in last_discovery_errors

Consolidate three tool stores into one (_tool_catalog)

Clean up dead code, fix two bugs, remove unused abstractions

Align project layout with HF Spaces and FastMCP conventions